0.018093
0.000000
0.000000
0.000000
0.009845
0.000000
0.000000
0.000000
0.008960
0.00000
0.00000
0.00000
Colussi, T.M.
Costantino, D.A.
Hammond, J.A.
Ruehle, G.M.
Nix, J.C.
Kieft, J.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
55.270
101.570
111.610
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H13 N5 O9 P2
409.186
n
ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
H18 Ir N6 3
294.400
IRIDIUM HEXAMMINE ION
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C10 H26 N4
202.340
SPERMINE
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
S
P
N
39
N
O
N
40
N
O
N
41
N
P
N
42
N
O
N
43
N
O
N
44
N
O
N
45
N
O
N
46
N
C
N
47
R
C
N
48
N
O
N
49
R
C
N
50
N
O
N
51
R
C
N
52
N
O
N
53
R
C
Y
54
N
N
Y
55
N
C
Y
56
N
N
Y
57
N
C
Y
58
N
C
N
59
N
N
Y
60
N
N
Y
61
N
C
Y
62
N
N
Y
63
N
C
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
O
N
78
N
P
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
O
N
85
S
C
N
86
N
O
N
87
R
C
N
88
N
O
N
89
R
C
N
90
N
N
N
91
N
C
N
92
N
O
N
93
N
N
N
94
N
C
N
95
N
N
N
96
N
C
N
97
N
C
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
O
N
113
N
P
N
114
N
O
N
115
N
O
N
116
N
O
N
117
N
C
N
118
R
C
N
119
N
O
N
120
S
C
N
121
N
O
N
122
R
C
N
123
N
O
N
124
R
C
Y
125
N
N
Y
126
N
C
Y
127
N
N
Y
128
N
C
N
129
N
C
N
130
N
O
N
131
N
N
N
132
N
C
N
133
N
N
N
134
N
N
Y
135
N
C
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
O
N
151
N
H
N
152
N
H
N
153
N
IR
N
154
N
N
N
155
N
N
N
156
N
N
N
157
N
N
N
158
N
N
N
159
N
N
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
MG
N
179
N
N
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
N
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
N
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
N
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
O
N
220
N
P
N
221
N
O
N
222
N
O
N
223
N
O
N
224
N
C
N
225
R
C
N
226
N
O
N
227
S
C
N
228
N
O
N
229
R
C
N
230
N
O
N
231
R
C
N
232
N
N
N
233
N
C
N
234
N
O
N
235
N
N
N
236
N
C
N
237
N
O
N
238
N
C
N
239
N
C
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
doub
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
Y
67
N
sing
Y
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
sing
Y
72
N
sing
Y
73
N
doub
N
74
N
sing
Y
75
N
doub
N
76
N
sing
N
77
N
sing
Y
78
N
sing
Y
79
N
doub
N
80
N
sing
Y
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
Y
142
N
sing
Y
143
N
sing
Y
144
N
doub
N
145
N
sing
Y
146
N
sing
N
147
N
sing
Y
148
N
doub
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
doub
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
doub
N
256
N
sing
N
257
N
sing
UK
Nature
NATUAS
0006
1476-4687
511
366
369
10.1038/nature13378
24909993
The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.
2014
UK
J.Mol.Biol.
JMOBAK
0070
1089-8638
399
450
463
10.1016/j.jmb.2010.04.016
20398674
Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA.
2010
UK
Rna
RNARFU
2122
1469-9001
15
294
307
10.1261/rna.1360709
19144910
Comparison and functional implications of the 3D architectures of viral tRNA-like structures.
2009
10.2210/pdb4p5j/pdb
pdb_00004p5j
100
1
CMOS
2013-10-21
RDI CMOS_8M
Rosenbaum-Rock Si(111) sagitally focused monochromator
SINGLE WAVELENGTH
M
x-ray
1
1.0972
1.0
4.2.2
ALS
1.0972
SYNCHROTRON
ALS BEAMLINE 4.2.2
27593.316
Turnip yellow mosaic virus mRNA for the coat protein
1
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
294.400
IRIDIUM HEXAMMINE ION
12
syn
non-polymer
202.340
SPERMINE
1
syn
non-polymer
18.015
water
126
nat
water
no
yes
UUAGCUCGCCAGUUAGCGAGGUCUGUCUCGACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG
GAACC(A23)
UUAGCUCGCCAGUUAGCGAGGUCUGUCUCGACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG
GAACCA
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.84
56.76
VAPOR DIFFUSION, SITTING DROP
7.5
This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days.
277.15
-7.577
1
19
A
2
A
74
-1.992
A_G2:C74_A
1
-5.705
0.047
-0.454
-0.167
20.267
A
32
A
26
159.736
A_C32:U26_A
2
-11.904
1.425
-0.509
-4.552
-4.082
1
19
A
33
A
25
3.451
A_G33:C25_A
3
-10.801
-0.544
0.290
-0.175
4.091
1
20
A
34
A
24
1.044
A_A34:U24_A
4
-10.690
-0.335
0.206
-0.198
4.442
1
19
A
35
A
23
-1.403
A_C35:G23_A
5
-11.608
0.630
0.097
-0.310
3.564
1
20
A
36
A
22
-0.447
A_A36:U22_A
6
-12.961
-0.001
0.127
-0.260
-1.738
1
19
A
37
A
21
-3.293
A_G37:C21_A
7
-13.814
-0.357
0.126
-0.375
-8.553
1
20
A
38
A
20
-0.715
A_A38:U20_A
8
-18.129
0.040
-0.027
-0.109
1.016
1
28
A
39
A
19
-4.210
A_U39:G19_A
9
-12.385
2.214
0.128
-0.628
-5.815
1
19
A
3
A
18
0.997
A_C3:G18_A
10
-10.421
0.107
0.121
-0.179
-8.591
1
20
A
4
A
17
1.543
A_U4:A17_A
11
-8.080
0.126
0.181
-0.148
1.358
1
19
A
5
A
16
-0.333
A_C5:G16_A
12
-10.509
0.238
0.060
-0.114
1.396
1
19
A
6
A
15
-0.930
A_G6:C15_A
13
-8.745
-0.145
0.189
-0.117
7.866
1
19
A
7
A
14
-0.066
A_C7:G14_A
14
-9.586
0.220
0.057
-0.209
13.023
2
15
A
8
A
52
178.881
A_C8:C52_A
15
36.275
1.714
0.141
1.536
-18.919
10
11
A
9
A
48
-3.130
A_A9:G48_A
16
11.398
-6.824
0.252
-4.451
-1.412
4
24
A
51
A
47
-99.833
A_A51:U47_A
17
1.528
-4.111
0.237
-1.972
5.993
1
19
A
54
A
46
1.029
A_C54:G46_A
18
-10.333
0.208
0.149
-0.213
6.301
1
19
A
55
A
45
-0.242
A_C55:G45_A
19
-12.443
0.006
-0.101
-0.082
4.102
1
19
A
56
A
44
0.079
A_C56:G44_A
20
-8.539
0.347
0.106
-0.134
0.185
1
19
A
57
A
43
-2.062
A_G57:C43_A
21
-7.899
-0.119
-0.129
-0.078
9.026
1
19
A
58
A
72
-4.008
A_C58:G72_A
22
-7.634
0.287
0.060
-0.175
5.047
1
19
A
59
A
71
2.019
A_C59:G71_A
23
-22.420
0.251
0.295
-0.260
-5.996
1
19
A
60
A
70
-2.478
A_C60:G70_A
24
-12.674
0.280
0.454
-0.158
-7.351
1
20
A
76
A
69
8.204
A_U76:A69_A
25
-0.087
-0.004
0.190
-0.215
1.397
1
19
A
77
A
68
-0.649
A_C77:G68_A
26
-14.115
0.210
0.058
-0.157
0.546
1
19
A
78
A
67
2.152
A_G78:C67_A
27
-12.071
-0.312
0.341
-0.170
2.602
1
19
A
79
A
66
-1.896
A_G79:C66_A
28
-14.544
0.027
0.158
-0.197
-3.422
1
20
A
80
A
65
0.229
A_A80:U65_A
29
-21.936
-0.089
-0.026
-0.139
-7.895
1
20
A
81
A
64
2.229
A_A81:U64_A
30
-10.081
0.075
0.294
-0.043
-7.828
2
15
A
83
A
63
-177.492
A_C83:C63_A
31
-6.595
-2.033
-0.341
-1.234
-27.199
1
19
A
10
A
49
0.771
A_G10:C49_A
32
-20.643
-0.173
-0.135
-0.083
3.054
130.572
A
A
32
33
-2.862
A
A
26
25
3.055
-5.199
0.909
-0.302
AA_C32G33:C25U26_AA
1
-1.786
0.983
130.512
-0.131
-0.513
2.975
34.018
A
A
33
34
4.032
A
A
25
24
3.045
2.355
-0.289
-1.130
AA_G33A34:U24C25_AA
2
-2.351
4.024
33.859
-2.278
0.149
2.928
36.007
A
A
34
35
9.960
A
A
24
23
3.234
6.129
-0.004
-1.592
AA_A34C35:G23U24_AA
3
0.030
-0.049
35.498
-3.402
0.011
2.248
29.596
A
A
35
36
23.045
A
A
23
22
3.114
11.475
-0.121
-1.665
AA_C35A36:U22G23_AA
4
-0.641
1.287
27.319
-5.335
0.122
2.780
34.359
A
A
36
37
15.634
A
A
22
21
3.251
9.129
-0.294
-1.427
AA_A36G37:C21U22_AA
5
-1.264
2.165
33.136
-3.758
0.312
3.153
35.273
A
A
37
38
11.425
A
A
21
20
3.425
6.874
0.410
-1.231
AA_G37A38:U20C21_AA
6
2.902
-4.823
34.500
-3.069
-0.239
2.727
39.794
A
A
38
39
10.720
A
A
20
19
3.001
7.255
0.051
-1.290
AA_A38U39:G19U20_AA
7
2.358
-3.484
39.085
-2.638
0.166
2.951
48.947
A
A
39
3
9.257
A
A
19
18
3.175
7.642
-2.106
-1.211
AA_U39C3:G18G19_AA
8
0.279
-0.338
48.382
-2.007
2.562
2.724
30.911
A
A
3
4
15.417
A
A
18
17
3.233
8.125
-0.445
-1.549
AA_C3U4:A17G18_AA
9
0.164
-0.312
29.849
-4.366
0.864
2.948
29.232
A
A
4
5
3.385
A
A
17
16
3.044
1.706
0.078
-1.543
AA_U4C5:G16A17_AA
10
2.212
-4.389
29.101
-3.398
0.285
2.579
31.422
A
A
5
6
16.650
A
A
16
15
3.149
8.899
0.153
-1.610
AA_C5G6:C15G16_AA
11
-0.291
0.544
30.164
-4.464
-0.332
3.230
33.644
A
A
6
7
-0.849
A
A
15
14
3.190
-0.491
0.458
-1.432
AA_G6C7:G14C15_AA
12
1.836
-3.173
33.592
-2.395
-0.498
2.542
-57.744
A
A
7
8
4.923
A
A
14
52
2.619
-4.745
0.602
-1.434
AA_C7C8:C52G14_AA
13
-4.812
-4.993
-57.381
1.686
0.419
-0.996
-7.127
A
A
9
51
-9.863
A
A
48
47
2.902
0.926
-2.013
-0.134
AA_A9A51:U47G48_AA
14
-6.725
-71.595
-2.173
-0.449
-27.277
2.961
89.360
A
A
51
54
2.699
A
A
47
46
3.091
3.794
1.873
-2.124
AA_A51C54:G46U47_AA
15
-3.371
2.398
89.246
-1.583
-1.396
2.835
32.214
A
A
54
55
7.723
A
A
46
45
3.111
4.273
-0.649
-2.083
AA_C54C55:G45G46_AA
16
-1.065
1.925
31.920
-4.449
0.996
3.032
31.129
A
A
55
56
8.838
A
A
45
44
3.313
4.719
-0.434
-1.824
AA_C55C56:G44G45_AA
17
-2.910
5.450
30.643
-4.281
0.264
3.010
32.207
A
A
56
57
9.989
A
A
44
43
3.362
5.515
0.176
-1.808
AA_C56G57:C43G44_AA
18
-0.495
0.896
31.740
-4.225
-0.404
2.977
39.303
A
A
57
58
0.734
A
A
43
72
3.020
0.493
0.272
-1.284
AA_G57C58:G72C43_AA
19
-2.943
4.379
39.195
-1.962
-0.726
2.727
38.123
A
A
58
59
15.719
A
A
72
71
3.115
10.151
1.000
-1.214
AA_C58C59:G71G72_AA
20
1.177
-1.823
36.777
-3.028
-1.395
2.909
36.308
A
A
59
60
12.291
A
A
71
70
3.329
7.604
-0.032
-1.717
AA_C59C60:G70G71_AA
21
1.273
-2.057
35.507
-3.781
0.222
1.665
36.601
A
A
60
76
20.098
A
A
70
69
2.855
12.376
-0.737
-2.949
AA_C60U76:A69G70_AA
22
2.874
-4.668
34.396
-5.911
1.456
3.230
29.300
A
A
76
77
-9.055
A
A
69
68
3.070
-4.557
-0.873
-0.895
AA_U76C77:G68A69_AA
23
-2.390
4.748
28.854
-0.815
1.225
1.983
30.804
A
A
77
78
25.092
A
A
68
67
3.013
12.914
-0.265
-1.885
AA_C77G78:C67G68_AA
24
-2.918
5.670
27.876
-5.575
0.041
2.791
35.720
A
A
78
79
13.084
A
A
67
66
3.125
7.962
-0.356
-1.221
AA_G78G79:C66C67_AA
25
-0.317
0.521
34.849
-3.045
0.538
3.173
35.167
A
A
79
80
9.126
A
A
66
65
3.377
5.486
0.144
-1.098
AA_G79A80:U65C66_AA
26
3.016
-5.016
34.622
-2.644
0.215
3.379
32.130
A
A
80
81
2.480
A
A
65
64
3.313
1.367
0.956
-0.839
AA_A80A81:U64U65_AA
27
4.814
-8.732
31.748
-1.767
-0.840
0.477
-163.456
A
A
81
83
66.690
A
A
64
63
-0.672
-128.191
6.554
-2.690
AA_A81C83:C63U64_AA
28
-87.609
-45.578
-95.580
1.328
3.332
citation
pdbx_audit_support
pdbx_database_status
pdbx_entity_src_syn
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
pdbx_validate_close_contact
pdbx_audit_support
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
refine_hist
struct_conn
struct_conn_type
repository
Initial release
Database references
Database references
Database references
Advisory
Author supporting evidence
Database references
Derived calculations
Other
Source and taxonomy
Author supporting evidence
Data collection
Database references
Derived calculations
Refinement description
1
0
2014-06-04
1
1
2014-06-25
1
2
2014-07-30
1
3
2014-10-01
1
4
2017-09-06
1
5
2019-11-20
1
6
2023-12-27
_citation.journal_id_CSD
_pdbx_audit_support.funding_organization
_pdbx_database_status.pdb_format_compatible
_pdbx_entity_src_syn.pdbx_alt_source_flag
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_oper_list.symmetry_operation
_pdbx_audit_support.funding_organization
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
United States
Howard Hughes Medical Institute (HHMI)
United States
National Institutes of Health/National Cancer Institute (NIH/NCI)
P30CA046934
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM081346
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM097333
United States
Department of Energy (DOE, United States)
DE-AC02-05CH11231
N
RCSB
Y
RCSB
2014-03-17
REL
REL
MG
MAGNESIUM ION
IRI
IRIDIUM HEXAMMINE ION
SPM
SPERMINE
HOH
water
RNA was prepared by in vitro transcription with T7 RNA polymerase
12154
Turnip yellow mosaic virus
sample
1
86
MG
1
2
MG
MG
101
A
MG
1
2
MG
MG
102
A
IRI
1
3
IRI
IRI
103
A
IRI
1
3
IRI
IRI
104
A
IRI
1
3
IRI
IRI
105
A
IRI
1
3
IRI
IRI
106
A
IRI
1
3
IRI
IRI
107
A
IRI
1
3
IRI
IRI
108
A
IRI
1
3
IRI
IRI
109
A
IRI
1
3
IRI
IRI
110
A
IRI
1
3
IRI
IRI
111
A
IRI
1
3
IRI
IRI
112
A
IRI
1
3
IRI
IRI
113
A
IRI
1
3
IRI
IRI
114
A
SPM
1
4
SPM
SPM
115
A
HOH
16
5
HOH
HOH
201
A
HOH
40
5
HOH
HOH
202
A
HOH
61
5
HOH
HOH
203
A
HOH
15
5
HOH
HOH
204
A
HOH
62
5
HOH
HOH
205
A
HOH
43
5
HOH
HOH
206
A
HOH
72
5
HOH
HOH
207
A
HOH
58
5
HOH
HOH
208
A
HOH
46
5
HOH
HOH
209
A
HOH
112
5
HOH
HOH
210
A
HOH
19
5
HOH
HOH
211
A
HOH
53
5
HOH
HOH
212
A
HOH
29
5
HOH
HOH
213
A
HOH
45
5
HOH
HOH
214
A
HOH
48
5
HOH
HOH
215
A
HOH
22
5
HOH
HOH
216
A
HOH
49
5
HOH
HOH
217
A
HOH
44
5
HOH
HOH
218
A
HOH
31
5
HOH
HOH
219
A
HOH
57
5
HOH
HOH
220
A
HOH
120
5
HOH
HOH
221
A
HOH
54
5
HOH
HOH
222
A
HOH
123
5
HOH
HOH
223
A
HOH
1
5
HOH
HOH
224
A
HOH
2
5
HOH
HOH
225
A
HOH
3
5
HOH
HOH
226
A
HOH
4
5
HOH
HOH
227
A
HOH
5
5
HOH
HOH
228
A
HOH
6
5
HOH
HOH
229
A
HOH
7
5
HOH
HOH
230
A
HOH
8
5
HOH
HOH
231
A
HOH
9
5
HOH
HOH
232
A
HOH
10
5
HOH
HOH
233
A
HOH
11
5
HOH
HOH
234
A
HOH
12
5
HOH
HOH
235
A
HOH
13
5
HOH
HOH
236
A
HOH
14
5
HOH
HOH
237
A
HOH
17
5
HOH
HOH
238
A
HOH
18
5
HOH
HOH
239
A
HOH
20
5
HOH
HOH
240
A
HOH
21
5
HOH
HOH
241
A
HOH
23
5
HOH
HOH
242
A
HOH
24
5
HOH
HOH
243
A
HOH
25
5
HOH
HOH
244
A
HOH
26
5
HOH
HOH
245
A
HOH
27
5
HOH
HOH
246
A
HOH
28
5
HOH
HOH
247
A
HOH
30
5
HOH
HOH
248
A
HOH
32
5
HOH
HOH
249
A
HOH
33
5
HOH
HOH
250
A
HOH
34
5
HOH
HOH
251
A
HOH
35
5
HOH
HOH
252
A
HOH
36
5
HOH
HOH
253
A
HOH
37
5
HOH
HOH
254
A
HOH
38
5
HOH
HOH
255
A
HOH
39
5
HOH
HOH
256
A
HOH
41
5
HOH
HOH
257
A
HOH
42
5
HOH
HOH
258
A
HOH
47
5
HOH
HOH
259
A
HOH
50
5
HOH
HOH
260
A
HOH
51
5
HOH
HOH
261
A
HOH
52
5
HOH
HOH
262
A
HOH
55
5
HOH
HOH
263
A
HOH
56
5
HOH
HOH
264
A
HOH
59
5
HOH
HOH
265
A
HOH
60
5
HOH
HOH
266
A
HOH
63
5
HOH
HOH
267
A
HOH
64
5
HOH
HOH
268
A
HOH
65
5
HOH
HOH
269
A
HOH
66
5
HOH
HOH
270
A
HOH
67
5
HOH
HOH
271
A
HOH
68
5
HOH
HOH
272
A
HOH
69
5
HOH
HOH
273
A
HOH
70
5
HOH
HOH
274
A
HOH
71
5
HOH
HOH
275
A
HOH
73
5
HOH
HOH
276
A
HOH
74
5
HOH
HOH
277
A
HOH
75
5
HOH
HOH
278
A
HOH
76
5
HOH
HOH
279
A
HOH
77
5
HOH
HOH
280
A
HOH
78
5
HOH
HOH
281
A
HOH
79
5
HOH
HOH
282
A
HOH
80
5
HOH
HOH
283
A
HOH
81
5
HOH
HOH
284
A
HOH
82
5
HOH
HOH
285
A
HOH
83
5
HOH
HOH
286
A
HOH
84
5
HOH
HOH
287
A
HOH
85
5
HOH
HOH
288
A
HOH
86
5
HOH
HOH
289
A
HOH
87
5
HOH
HOH
290
A
HOH
88
5
HOH
HOH
291
A
HOH
89
5
HOH
HOH
292
A
HOH
90
5
HOH
HOH
293
A
HOH
91
5
HOH
HOH
294
A
HOH
92
5
HOH
HOH
295
A
HOH
93
5
HOH
HOH
296
A
HOH
94
5
HOH
HOH
297
A
HOH
95
5
HOH
HOH
298
A
HOH
96
5
HOH
HOH
299
A
HOH
97
5
HOH
HOH
300
A
HOH
98
5
HOH
HOH
301
A
HOH
99
5
HOH
HOH
302
A
HOH
100
5
HOH
HOH
303
A
HOH
101
5
HOH
HOH
304
A
HOH
102
5
HOH
HOH
305
A
HOH
103
5
HOH
HOH
306
A
HOH
104
5
HOH
HOH
307
A
HOH
105
5
HOH
HOH
308
A
HOH
106
5
HOH
HOH
309
A
HOH
107
5
HOH
HOH
310
A
HOH
108
5
HOH
HOH
311
A
HOH
109
5
HOH
HOH
312
A
HOH
110
5
HOH
HOH
313
A
HOH
111
5
HOH
HOH
314
A
HOH
113
5
HOH
HOH
315
A
HOH
114
5
HOH
HOH
316
A
HOH
115
5
HOH
HOH
317
A
HOH
116
5
HOH
HOH
318
A
HOH
117
5
HOH
HOH
319
A
HOH
118
5
HOH
HOH
320
A
HOH
119
5
HOH
HOH
321
A
HOH
121
5
HOH
HOH
322
A
HOH
122
5
HOH
HOH
323
A
HOH
124
5
HOH
HOH
324
A
HOH
125
5
HOH
HOH
325
A
HOH
126
5
HOH
HOH
326
A
n
1
-1
A
n
2
0
A
A
1
n
3
A
1
A
G
2
n
4
G
2
A
C
3
n
5
C
3
A
U
4
n
6
U
4
A
C
5
n
7
C
5
A
G
6
n
8
G
6
A
C
7
n
9
C
7
A
C
8
n
10
C
8
A
A
9
n
11
A
9
A
G
10
n
12
G
10
A
U
11
n
13
U
11
A
U
12
n
14
U
12
A
A
13
n
15
A
13
A
G
14
n
16
G
14
A
C
15
n
17
C
15
A
G
16
n
18
G
16
A
A
17
n
19
A
17
A
G
18
n
20
G
18
A
G
19
n
21
G
19
A
U
20
n
22
U
20
A
C
21
n
23
C
21
A
U
22
n
24
U
22
A
G
23
n
25
G
23
A
U
24
n
26
U
24
A
C
25
n
27
C
25
A
U
26
n
28
U
26
A
C
27
n
29
C
27
A
G
28
n
30
G
28
A
A
29
n
31
A
29
A
C
30
n
32
C
30
A
A
31
n
33
A
31
A
C
32
n
34
C
32
A
G
33
n
35
G
33
A
A
34
n
36
A
34
A
C
35
n
37
C
35
A
A
36
n
38
A
36
A
G
37
n
39
G
37
A
A
38
n
40
A
38
A
U
39
n
41
U
39
A
A
40
n
42
A
40
A
A
41
n
43
A
41
A
U
42
n
44
U
42
A
C
43
n
45
C
43
A
G
44
n
46
G
44
A
G
45
n
47
G
45
A
G
46
n
48
G
46
A
U
47
n
49
U
47
A
G
48
n
50
G
48
A
C
49
n
51
C
49
A
A
50
n
52
A
50
A
A
51
n
53
A
51
A
C
52
n
54
C
52
A
U
53
n
55
U
53
A
C
54
n
56
C
54
A
C
55
n
57
C
55
A
C
56
n
58
C
56
A
G
57
n
59
G
57
A
C
58
n
60
C
58
A
C
59
n
61
C
59
A
C
60
n
62
C
60
A
C
61
n
63
C
61
A
U
62
n
64
U
62
A
C
63
n
65
C
63
A
U
64
n
66
U
64
A
U
65
n
67
U
65
A
C
66
n
68
C
66
A
C
67
n
69
C
67
A
G
68
n
70
G
68
A
A
69
n
71
A
69
A
G
70
n
72
G
70
A
G
71
n
73
G
71
A
G
72
n
74
G
72
A
U
73
n
75
U
73
A
C
74
n
76
C
74
A
A
75
n
77
A
75
A
U
76
n
78
U
76
A
C
77
n
79
C
77
A
G
78
n
80
G
78
A
G
79
n
81
G
79
A
A
80
n
82
A
80
A
A
81
n
83
A
81
A
C
82
n
84
C
82
A
C
83
n
85
C
83
A
A23
84
n
86
A23
84
A
author_and_software_defined_assembly
PISA
1
monomeric
4020
-40
14100
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
225
Q
O
HOH
1_555
90.7
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
228
Q
O
HOH
1_555
80.8
A
HOH
225
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
228
Q
O
HOH
1_555
78.2
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
244
Q
O
HOH
1_555
81.3
A
HOH
225
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
244
Q
O
HOH
1_555
152.8
A
HOH
228
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
244
Q
O
HOH
1_555
74.9
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
252
Q
O
HOH
1_555
156.8
A
HOH
225
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
252
Q
O
HOH
1_555
76.7
A
HOH
228
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
252
Q
O
HOH
1_555
77.6
A
HOH
244
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
252
Q
O
HOH
1_555
101.0
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
111.7
A
HOH
225
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
90.7
A
HOH
228
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
163.6
A
HOH
244
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
116.4
A
HOH
252
Q
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
88.2
A
HOH
224
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
226
Q
O
HOH
1_555
88.2
A
HOH
224
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
227
Q
O
HOH
1_555
88.8
A
HOH
226
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
227
Q
O
HOH
1_555
174.8
A
HOH
224
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
229
Q
O
HOH
1_555
172.6
A
HOH
226
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
229
Q
O
HOH
1_555
87.6
A
HOH
227
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
229
Q
O
HOH
1_555
95.9
A
HOH
224
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
236
Q
O
HOH
1_555
92.8
A
HOH
226
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
236
Q
O
HOH
1_555
93.1
A
HOH
227
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
236
Q
O
HOH
1_555
82.9
A
HOH
229
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
236
Q
O
HOH
1_555
93.4
A
HOH
224
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
94.2
A
HOH
226
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
91.5
A
HOH
227
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
92.9
A
HOH
229
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
79.9
A
HOH
236
Q
O
HOH
1_555
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
171.7
A
A23
84
modified residue
A
A23
86
A
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
HOH
219
Q
HOH
1
A
U
-1
A
U
1
1
Y
1
A
U
0
A
U
2
1
Y
1
A
A
O6
O
G
HOH
23
324
2.14
1
A
A
O2
N3
U
IRI
26
104
2.17
1
A
A
N1
O
IRI
HOH
104
311
2.19
1
A
G
48
0.049
SIDE CHAIN
1
-4.48
0.70
118.00
113.52
A
A
A
N3
C4
N4
C
C
C
5
5
5
N
1
-5.11
0.80
109.40
104.29
A
A
A
O5'
C5'
C4'
A
A
A
9
9
9
N
1
-2.75
0.40
110.80
108.05
A
A
A
C4
C5
N7
G
G
G
10
10
10
N
1
4.88
0.70
108.50
113.38
A
A
A
O4'
C1'
N1
U
U
U
12
12
12
N
1
2.89
0.40
106.40
109.29
A
A
A
C8
N9
C4
G
G
G
14
14
14
N
1
-4.17
0.50
113.10
108.93
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
1
3.51
0.40
106.40
109.91
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
1
4.20
0.60
119.90
124.10
A
A
A
N1
C6
O6
G
G
G
16
16
16
N
1
-4.62
0.60
128.60
123.98
A
A
A
C5
C6
O6
G
G
G
16
16
16
N
1
-4.65
0.60
128.60
123.95
A
A
A
C5
C6
O6
G
G
G
23
23
23
N
1
-5.97
0.90
105.70
99.73
A
A
A
O5'
P
OP2
U
U
U
42
42
42
N
1
-4.02
0.60
127.00
122.98
A
A
A
C2
N3
C4
U
U
U
42
42
42
N
1
9.03
1.50
119.60
128.63
A
A
A
OP1
P
OP2
G
G
G
48
48
48
N
1
4.99
0.50
111.90
116.89
A
A
A
C2
N3
C4
G
G
G
48
48
48
N
1
-3.19
0.50
128.60
125.41
A
A
A
N3
C4
C5
G
G
G
48
48
48
N
1
-3.05
0.50
110.60
107.55
A
A
A
C2
N3
C4
A
A
A
50
50
50
N
1
3.64
0.60
118.60
122.24
A
A
A
N1
C6
N6
A
A
A
50
50
50
N
1
2.86
0.40
105.80
108.66
A
A
A
C8
N9
C4
A
A
A
51
51
51
N
1
6.86
1.10
110.50
117.36
A
A
A
O3'
P
OP1
A
C
C
51
52
52
Y
1
6.82
1.10
110.50
117.32
A
A
A
O3'
P
OP2
C
C
C
58
59
59
Y
1
-5.31
0.60
118.90
113.59
A
A
A
N1
C2
O2
C
C
C
60
60
60
N
1
-6.43
0.90
105.70
99.27
A
A
A
O5'
P
OP2
U
U
U
62
62
62
N
1
-4.93
0.70
118.00
113.07
A
A
A
N3
C4
N4
C
C
C
63
63
63
N
1
-11.00
0.90
105.70
94.70
A
A
A
O5'
P
OP2
G
G
G
70
70
70
N
1
-6.59
0.90
105.70
99.11
A
A
A
O5'
P
OP1
G
G
G
71
71
71
N
1
4.23
0.60
119.90
124.13
A
A
A
N1
C6
O6
G
G
G
71
71
71
N
1
-4.64
0.60
128.60
123.96
A
A
A
C5
C6
O6
G
G
G
71
71
71
N
1
4.43
0.60
118.60
123.03
A
A
A
C6
N1
C2
A
A
A
75
75
75
N
1
-3.37
0.50
129.30
125.93
A
A
A
N1
C2
N3
A
A
A
75
75
75
N
1
3.62
0.60
121.00
124.62
A
A
A
C6
N1
C2
U
U
U
76
76
76
N
1
6.20
0.90
109.80
116.00
A
A
A
C5'
C4'
O4'
C
C
C
77
77
77
N
1
16.71
1.10
110.50
127.21
A
A
A
O3'
P
OP2
C
A23
A23
83
84
84
Y
1
A
A
N3
C4
A
A
51
51
0.036
0.006
1.344
1.380
N
0.2396
0.2057
0.2088
1.9912
28.871
3790
41334
9.17
99.46
0.23
Random
1
FREE R-VALUE
1.34
SAD
27.57
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
1.9912
28.871
126
2011
100
1785
0
0.011
2078
1.791
3295
14.148
1042
0.082
420
0.013
84
0.3259
0.3046
2.0164
126
1239
90.00
0.3908
0.2973
2.0430
139
1395
100.00
0.3024
0.2883
2.0709
148
1410
100.00
0.3230
0.2830
2.1005
136
1379
100.00
0.2785
0.2746
2.1319
140
1391
100.00
0.2982
0.2567
2.1652
140
1396
100.00
0.2496
0.2360
2.2007
139
1388
100.00
0.2812
0.2346
2.2386
143
1410
100.00
0.2925
0.2277
2.2793
143
1401
100.00
0.2641
0.2262
2.3231
138
1363
100.00
0.2825
0.2316
2.3705
143
1413
100.00
0.2770
0.2279
2.4220
142
1419
100.00
0.2489
0.2295
2.4783
141
1377
100.00
0.3312
0.2501
2.5403
143
1396
100.00
0.2752
0.2497
2.6089
142
1396
100.00
0.2989
0.2521
2.6856
143
1404
100.00
0.2850
0.2557
2.7722
147
1400
100.00
0.2994
0.2741
2.8712
142
1395
100.00
0.3721
0.2373
2.9861
133
1391
100.00
0.2124
0.2053
3.1218
143
1404
100.00
0.2412
0.1825
3.2862
136
1403
100.00
0.2382
0.1804
3.4918
141
1413
100.00
0.1896
0.1743
3.7608
139
1369
100.00
0.2050
0.1764
4.1383
143
1421
100.00
0.1714
0.1695
4.7349
144
1387
100.00
0.2057
0.1556
5.9568
138
1392
100.00
0.2058
0.2029
28.8736
138
1392
98.00
1.99
66.0
4P5J
41343
2.0
.054
1
21.71
7.45
99.4
.82
1.99
2.03
2.19
1
94.7
refinement
PHENIX
(phenix.refine: 1.8.4_1496)
Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
5
N
N
covale
1.592
both
A
C
83
A
O3'
C
85
1_555
A
A23
84
A
P
A23
86
1_555
metalc
2.013
A
A
40
A
OP2
A
42
1_555
A
MG
102
C
MG
MG
1_555
metalc
2.033
A
MG
101
B
MG
MG
1_555
A
HOH
224
Q
O
HOH
1_555
metalc
2.129
A
MG
101
B
MG
MG
1_555
A
HOH
226
Q
O
HOH
1_555
metalc
2.021
A
MG
101
B
MG
MG
1_555
A
HOH
227
Q
O
HOH
1_555
metalc
2.332
A
MG
101
B
MG
MG
1_555
A
HOH
229
Q
O
HOH
1_555
metalc
2.103
A
MG
101
B
MG
MG
1_555
A
HOH
236
Q
O
HOH
1_555
metalc
2.197
A
MG
101
B
MG
MG
1_555
A
HOH
237
Q
O
HOH
1_555
metalc
2.249
A
MG
102
C
MG
MG
1_555
A
HOH
225
Q
O
HOH
1_555
metalc
2.376
A
MG
102
C
MG
MG
1_555
A
HOH
228
Q
O
HOH
1_555
metalc
2.123
A
MG
102
C
MG
MG
1_555
A
HOH
244
Q
O
HOH
1_555
metalc
2.238
A
MG
102
C
MG
MG
1_555
A
HOH
252
Q
O
HOH
1_555
metalc
2.144
A
MG
102
C
MG
MG
1_555
A
HOH
273
Q
O
HOH
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
4
1_555
A
C
74
A
N3
C
76
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
4
1_555
A
C
74
A
O2
C
76
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
4
1_555
A
C
74
A
N4
C
76
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
5
1_555
A
G
18
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
5
1_555
A
G
18
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
5
1_555
A
G
18
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
6
1_555
A
A
17
A
N1
A
19
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
6
1_555
A
A
17
A
N6
A
19
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
7
1_555
A
G
16
A
N1
G
18
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
7
1_555
A
G
16
A
O6
G
18
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
7
1_555
A
G
16
A
N2
G
18
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
8
1_555
A
C
15
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
8
1_555
A
C
15
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
8
1_555
A
C
15
A
N4
C
17
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
9
1_555
A
G
14
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
9
1_555
A
G
14
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
9
1_555
A
G
14
A
N2
G
16
1_555
hydrog
TYPE_15_PAIR
A
C
8
A
N4
C
10
1_555
A
C
52
A
O2
C
54
1_555
hydrog
TYPE_15_PAIR
A
C
8
A
O2
C
10
1_555
A
C
52
A
N4
C
54
1_555
hydrog
TYPE_11_PAIR
A
A
9
A
N6
A
11
1_555
A
G
48
A
N3
G
50
1_555
hydrog
TYPE_11_PAIR
A
A
9
A
N7
A
11
1_555
A
G
48
A
N2
G
50
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
12
1_555
A
C
49
A
N3
C
51
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
12
1_555
A
C
49
A
O2
C
51
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
12
1_555
A
C
49
A
N4
C
51
1_555
hydrog
TYPE_28_PAIR
A
G
19
A
N1
G
21
1_555
A
U
39
A
O2
U
41
1_555
hydrog
TYPE_28_PAIR
A
G
19
A
O6
G
21
1_555
A
U
39
A
N3
U
41
1_555
hydrog
WATSON-CRICK
A
U
20
A
N3
U
22
1_555
A
A
38
A
N1
A
40
1_555
hydrog
WATSON-CRICK
A
U
20
A
O4
U
22
1_555
A
A
38
A
N6
A
40
1_555
hydrog
WATSON-CRICK
A
C
21
A
N3
C
23
1_555
A
G
37
A
N1
G
39
1_555
hydrog
WATSON-CRICK
A
C
21
A
N4
C
23
1_555
A
G
37
A
O6
G
39
1_555
hydrog
WATSON-CRICK
A
C
21
A
O2
C
23
1_555
A
G
37
A
N2
G
39
1_555
hydrog
WATSON-CRICK
A
U
22
A
N3
U
24
1_555
A
A
36
A
N1
A
38
1_555
hydrog
WATSON-CRICK
A
U
22
A
O4
U
24
1_555
A
A
36
A
N6
A
38
1_555
hydrog
WATSON-CRICK
A
G
23
A
N1
G
25
1_555
A
C
35
A
N3
C
37
1_555
hydrog
WATSON-CRICK
A
G
23
A
N2
G
25
1_555
A
C
35
A
O2
C
37
1_555
hydrog
WATSON-CRICK
A
G
23
A
O6
G
25
1_555
A
C
35
A
N4
C
37
1_555
hydrog
WATSON-CRICK
A
U
24
A
N3
U
26
1_555
A
A
34
A
N1
A
36
1_555
hydrog
WATSON-CRICK
A
U
24
A
O4
U
26
1_555
A
A
34
A
N6
A
36
1_555
hydrog
WATSON-CRICK
A
C
25
A
N3
C
27
1_555
A
G
33
A
N1
G
35
1_555
hydrog
WATSON-CRICK
A
C
25
A
N4
C
27
1_555
A
G
33
A
O6
G
35
1_555
hydrog
WATSON-CRICK
A
C
25
A
O2
C
27
1_555
A
G
33
A
N2
G
35
1_555
hydrog
U-C MISPAIR
A
U
26
A
O4
U
28
1_555
A
C
32
A
N4
C
34
1_555
hydrog
WATSON-CRICK
A
C
43
A
N3
C
45
1_555
A
G
57
A
N1
G
59
1_555
hydrog
WATSON-CRICK
A
C
43
A
N4
C
45
1_555
A
G
57
A
O6
G
59
1_555
hydrog
WATSON-CRICK
A
C
43
A
O2
C
45
1_555
A
G
57
A
N2
G
59
1_555
hydrog
WATSON-CRICK
A
G
44
A
N1
G
46
1_555
A
C
56
A
N3
C
58
1_555
hydrog
WATSON-CRICK
A
G
44
A
N2
G
46
1_555
A
C
56
A
O2
C
58
1_555
hydrog
WATSON-CRICK
A
G
44
A
O6
G
46
1_555
A
C
56
A
N4
C
58
1_555
hydrog
WATSON-CRICK
A
G
45
A
N1
G
47
1_555
A
C
55
A
N3
C
57
1_555
hydrog
WATSON-CRICK
A
G
45
A
N2
G
47
1_555
A
C
55
A
O2
C
57
1_555
hydrog
WATSON-CRICK
A
G
45
A
O6
G
47
1_555
A
C
55
A
N4
C
57
1_555
hydrog
WATSON-CRICK
A
G
46
A
N1
G
48
1_555
A
C
54
A
N3
C
56
1_555
hydrog
WATSON-CRICK
A
G
46
A
N2
G
48
1_555
A
C
54
A
O2
C
56
1_555
hydrog
WATSON-CRICK
A
G
46
A
O6
G
48
1_555
A
C
54
A
N4
C
56
1_555
hydrog
REVERSED HOOGSTEEN
A
U
47
A
N3
U
49
1_555
A
A
51
A
N7
A
53
1_555
hydrog
REVERSED HOOGSTEEN
A
U
47
A
O2
U
49
1_555
A
A
51
A
N6
A
53
1_555
hydrog
WATSON-CRICK
A
C
58
A
N3
C
60
1_555
A
G
72
A
N1
G
74
1_555
hydrog
WATSON-CRICK
A
C
58
A
N4
C
60
1_555
A
G
72
A
O6
G
74
1_555
hydrog
WATSON-CRICK
A
C
58
A
O2
C
60
1_555
A
G
72
A
N2
G
74
1_555
hydrog
WATSON-CRICK
A
C
59
A
N3
C
61
1_555
A
G
71
A
N1
G
73
1_555
hydrog
WATSON-CRICK
A
C
59
A
N4
C
61
1_555
A
G
71
A
O6
G
73
1_555
hydrog
WATSON-CRICK
A
C
59
A
O2
C
61
1_555
A
G
71
A
N2
G
73
1_555
hydrog
WATSON-CRICK
A
C
60
A
N3
C
62
1_555
A
G
70
A
N1
G
72
1_555
hydrog
WATSON-CRICK
A
C
60
A
N4
C
62
1_555
A
G
70
A
O6
G
72
1_555
hydrog
WATSON-CRICK
A
C
60
A
O2
C
62
1_555
A
G
70
A
N2
G
72
1_555
hydrog
C-C MISPAIR
A
C
61
A
O2
C
63
1_555
A
C
77
A
N4
C
79
1_555
hydrog
TYPE_15_PAIR
A
C
63
A
N4
C
65
1_555
A
C
83
A
O2
C
85
1_555
hydrog
TYPE_15_PAIR
A
C
63
A
O2
C
65
1_555
A
C
83
A
N4
C
85
1_555
hydrog
WATSON-CRICK
A
U
64
A
N3
U
66
1_555
A
A
81
A
N1
A
83
1_555
hydrog
WATSON-CRICK
A
U
64
A
O4
U
66
1_555
A
A
81
A
N6
A
83
1_555
hydrog
WATSON-CRICK
A
U
65
A
N3
U
67
1_555
A
A
80
A
N1
A
82
1_555
hydrog
WATSON-CRICK
A
U
65
A
O4
U
67
1_555
A
A
80
A
N6
A
82
1_555
hydrog
WATSON-CRICK
A
C
66
A
N3
C
68
1_555
A
G
79
A
N1
G
81
1_555
hydrog
WATSON-CRICK
A
C
66
A
N4
C
68
1_555
A
G
79
A
O6
G
81
1_555
hydrog
WATSON-CRICK
A
C
66
A
O2
C
68
1_555
A
G
79
A
N2
G
81
1_555
hydrog
WATSON-CRICK
A
C
67
A
N3
C
69
1_555
A
G
78
A
N1
G
80
1_555
hydrog
WATSON-CRICK
A
C
67
A
N4
C
69
1_555
A
G
78
A
O6
G
80
1_555
hydrog
WATSON-CRICK
A
C
67
A
O2
C
69
1_555
A
G
78
A
N2
G
80
1_555
hydrog
WATSON-CRICK
A
G
68
A
N1
G
70
1_555
A
C
77
A
N3
C
79
1_555
hydrog
WATSON-CRICK
A
G
68
A
N2
G
70
1_555
A
C
77
A
O2
C
79
1_555
hydrog
WATSON-CRICK
A
G
68
A
O6
G
70
1_555
A
C
77
A
N4
C
79
1_555
hydrog
WATSON-CRICK
A
A
69
A
N1
A
71
1_555
A
U
76
A
N3
U
78
1_555
hydrog
WATSON-CRICK
A
A
69
A
N6
A
71
1_555
A
U
76
A
O4
U
78
1_555
hydrog
G-A MISPAIR
A
G
71
A
N2
G
73
1_555
A
A
75
A
N3
A
77
1_555
RNA
tRNA-mimic viral RNA Pseudoknot multifunctional, RNA
V01418.1
GB
1
610
62226
UUAGCUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG
GAACCA
610
695
4P5J
-1
84
62226
A
1
1
86
1
C
conflict
U
26
4P5J
A
62226
GB
637
28
1
C
conflict
G
28
4P5J
A
62226
GB
639
30
binding site for residue MG A 101
A
MG
101
Software
6
binding site for residue MG A 102
A
MG
102
Software
6
binding site for residue IRI A 103
A
IRI
103
Software
11
binding site for residue IRI A 104
A
IRI
104
Software
4
binding site for residue IRI A 105
A
IRI
105
Software
10
binding site for residue IRI A 106
A
IRI
106
Software
6
binding site for residue IRI A 107
A
IRI
107
Software
3
binding site for residue IRI A 108
A
IRI
108
Software
5
binding site for residue IRI A 109
A
IRI
109
Software
6
binding site for residue IRI A 110
A
IRI
110
Software
3
binding site for residue IRI A 111
A
IRI
111
Software
6
binding site for residue IRI A 112
A
IRI
112
Software
3
binding site for residue IRI A 113
A
IRI
113
Software
4
binding site for residue IRI A 114
A
IRI
114
Software
5
binding site for residue SPM A 115
A
SPM
115
Software
5
A
HOH
224
Q
HOH
6
1_555
A
HOH
226
Q
HOH
6
1_555
A
HOH
227
Q
HOH
6
1_555
A
HOH
229
Q
HOH
6
1_555
A
HOH
236
Q
HOH
6
1_555
A
HOH
237
Q
HOH
6
1_555
A
A
40
A
A
42
6
1_555
A
HOH
225
Q
HOH
6
1_555
A
HOH
228
Q
HOH
6
1_555
A
HOH
244
Q
HOH
6
1_555
A
HOH
252
Q
HOH
6
1_555
A
HOH
273
Q
HOH
6
1_555
A
G
44
A
G
46
11
1_555
A
G
45
A
G
47
11
1_555
A
G
46
A
G
48
11
1_555
A
A
51
A
A
53
11
1_555
A
HOH
258
Q
HOH
11
1_555
A
HOH
272
Q
HOH
11
1_555
A
HOH
275
Q
HOH
11
1_555
A
HOH
284
Q
HOH
11
1_555
A
HOH
286
Q
HOH
11
1_555
A
HOH
287
Q
HOH
11
1_555
A
HOH
325
Q
HOH
11
1_555
A
U
26
A
U
28
4
1_555
A
C
30
A
C
32
4
1_555
A
HOH
311
Q
HOH
4
1_555
A
HOH
319
Q
HOH
4
1_555
A
C
56
A
C
58
10
1_555
A
G
57
A
G
59
10
1_555
A
C
58
A
C
60
10
1_555
A
G
71
A
G
73
10
1_555
A
G
72
A
G
74
10
1_555
A
HOH
248
Q
HOH
10
1_555
A
HOH
249
Q
HOH
10
1_555
A
HOH
290
Q
HOH
10
1_555
A
HOH
291
Q
HOH
10
1_555
A
HOH
310
Q
HOH
10
1_555
A
C
5
A
C
7
6
2_665
A
G
6
A
G
8
6
2_665
A
G
78
A
G
80
6
1_555
A
G
79
A
G
81
6
1_555
A
A23
84
A
A23
86
6
1_555
A
HOH
309
Q
HOH
6
1_555
A
G
45
A
G
47
3
2_565
A
C
60
A
C
62
3
1_555
A
U
62
A
U
64
3
1_555
A
U
47
A
U
49
5
1_555
A
G
48
A
G
50
5
1_555
A
A
50
A
A
52
5
1_555
A
HOH
203
Q
HOH
5
1_555
A
HOH
268
Q
HOH
5
1_555
A
A
17
A
A
19
6
1_555
A
G
18
A
G
20
6
1_555
A
G
19
A
G
21
6
1_555
A
U
39
A
U
41
6
1_555
A
HOH
282
Q
HOH
6
1_555
A
HOH
303
Q
HOH
6
1_555
A
C
60
A
C
62
3
1_555
A
C
61
A
C
63
3
1_555
A
A
75
A
A
77
3
1_555
A
C
43
A
C
45
6
1_555
A
G
44
A
G
46
6
1_555
A
G
57
A
G
59
6
1_555
A
C
58
A
C
60
6
1_555
A
C
59
A
C
61
6
1_555
A
U
73
A
U
75
6
1_555
A
A
1
A
A
3
3
3_655
A
G
2
A
G
4
3
3_655
A
U
22
A
U
24
3
1_555
A
U
11
A
U
13
4
1_555
A
U
12
A
U
14
4
1_555
A
G
28
A
G
30
4
3_655
A
C
83
A
C
85
4
7_555
A
G
14
A
G
16
5
1_555
A
U
39
A
U
41
5
1_555
A
A
40
A
A
42
5
1_555
A
A
41
A
A
43
5
1_555
A
HOH
273
Q
HOH
5
1_555
A
G
68
A
G
70
5
2_665
A
G
78
A
G
80
5
2_665
A
G
79
A
G
81
5
1_555
A
G
79
A
G
81
5
2_665
A
A
80
A
A
82
5
1_555
23
I 2 2 2