0.013038
0.007528
0.000000
0.000000
0.015055
0.000000
0.000000
0.000000
0.013081
0.00000
0.00000
0.00000
Chapman, E.G.
Costantino, D.A.
Rabe, J.L.
Moon, S.L.
Wilusz, J.
Nix, J.C.
Kieft, J.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
76.698
76.698
76.448
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
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
Mg 2
24.305
MAGNESIUM ION
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
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
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
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
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
O
N
112
N
H
N
113
N
H
N
114
N
MG
N
115
N
O
N
116
N
P
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
C
N
121
R
C
N
122
N
O
N
123
S
C
N
124
N
O
N
125
R
C
N
126
N
O
N
127
R
C
N
128
N
N
N
129
N
C
N
130
N
O
N
131
N
N
N
132
N
C
N
133
N
O
N
134
N
C
N
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
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
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
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
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
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
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
US
Science
SCIEAS
0038
0036-8075
344
307
310
10.1126/science.1250897
24744377
The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production.
2014
10.2210/pdb4pqv/pdb
pdb_00004pqv
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CMOS
2013-09-27
TAURUS-1
Rosenbaum-Rock sagitally focused Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.0972
1.0
4.2.2
ALS
1.0972
SYNCHROTRON
ALS BEAMLINE 4.2.2
22095.186
XRN1-resistant flaviviral RNA
U2G, G-U pair insertion
1
syn
polymer
24.305
MAGNESIUM ION
9
syn
non-polymer
18.015
water
7
nat
water
no
no
GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU
GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU
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
1
2.94
58.13
VAPOR DIFFUSION, SITTING DROP
7.5
drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 2 uL 10% MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine, 80 mM sodium chloride, 20 mM magnesium chloride (Nucleic Acid Mini-Screen kit, Hampton Research), well: 20-35% MPD, crystals appeared within 2-3 days and grew to full size over 1-2 weeks. To obtain derivatized crystals for phasing, 5 uL 4 mM iridium (III) hexammine in RNase-free water was added directly to crystallization drops and well solutions <35% MPD were replaced with 35% MPD. Wells were then re-sealed and allowed to re-equilibrate for at least 2 days, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
15.721
1
19
A
3
A
40
2.174
A_G3:C40_A
1
-1.973
-0.404
0.496
-0.309
-4.693
1
19
A
23
A
39
-1.097
A_C23:G39_A
2
-8.478
0.307
0.526
-0.616
8.694
3
23
A
24
A
4
60.777
A_A24:U4_A
3
-1.868
0.267
-0.608
-3.294
2.914
1
19
A
25
A
37
-3.839
A_C25:G37_A
4
-16.239
0.208
0.276
-0.204
8.783
1
20
A
26
A
36
-0.638
A_U26:A36_A
5
-24.847
-0.179
-0.554
-0.231
0.491
1
28
A
27
A
35
3.529
A_U27:G35_A
6
-20.504
2.230
0.216
-0.808
0.107
1
19
A
28
A
34
-0.550
A_C28:G34_A
7
-12.334
0.102
0.226
-0.441
-8.147
A
17
A
14
-56.245
A_A17:G14_A
8
-18.741
-8.168
1.091
-4.882
-3.679
1
19
A
18
A
13
-0.026
A_G18:C13_A
9
-7.974
-0.219
-0.302
-0.205
4.781
1
28
A
19
A
12
3.725
A_U19:G12_A
10
-8.794
2.285
-0.046
-0.026
-1.720
1
A
20
A
11
6.798
A_C20:G11_A
11
-16.407
0.182
0.356
0.480
29.904
1
19
A
21
A
10
-9.534
A_G21:C10_A
12
9.931
-0.246
0.175
0.119
28.332
1
20
A
42
A
9
-1.771
A_A42:U9_A
13
-10.192
0.661
0.659
-0.245
8.403
1
20
A
43
A
8
-0.035
A_U43:A8_A
14
-29.590
0.212
-0.415
0.133
-8.770
1
19
A
44
A
7
1.866
A_C44:G7_A
15
-10.454
-0.294
1.121
0.049
-5.782
1
20
A
45
A
6
4.130
A_U45:A6_A
16
-21.182
-0.474
0.427
0.154
-2.109
1
19
A
46
A
5
-7.901
A_G46:C5_A
17
-12.006
0.193
-0.159
-0.587
-2.989
3
23
A
47
A
49
-65.595
A_U47:A49_A
18
-9.508
-0.226
0.319
3.047
5.263
1
19
A
53
A
67
-3.873
A_C53:G67_A
19
-9.144
-0.319
-0.297
-0.471
7.914
1
19
A
54
A
66
-3.593
A_C54:G66_A
20
-15.760
-0.081
-0.456
-0.284
-4.887
1
19
A
55
A
65
-1.246
A_C55:G65_A
21
0.118
0.257
0.071
-0.064
0.851
1
20
A
56
A
64
3.083
A_A56:U64_A
22
-6.059
0.038
0.312
-0.161
-9.863
1
19
A
57
A
63
2.864
A_G57:C63_A
23
-10.603
-0.348
0.029
-0.317
2.834
10
11
A
58
A
62
-5.020
A_G58:A62_A
24
4.968
6.396
0.169
-4.419
3.638
54.562
A
A
3
23
7.347
A
A
40
39
3.599
6.712
-1.984
-0.858
AA_G3C23:G39C40_AA
1
-5.183
5.674
53.950
-1.388
1.816
2.905
-4.763
A
A
23
24
-20.246
A
A
39
4
3.485
1.610
0.352
0.024
AA_C23A24:U4G39_AA
2
1.691
21.268
-4.152
-14.166
18.822
2.204
57.449
A
A
24
25
10.748
A
A
4
37
2.827
10.277
-0.547
-3.728
AA_A24C25:G37U4_AA
3
-3.777
3.949
56.483
-4.312
0.410
2.157
30.894
A
A
25
26
20.322
A
A
37
36
3.039
10.596
-0.840
-1.800
AA_C25U26:A36G37_AA
4
3.192
-6.122
28.890
-5.069
2.087
3.291
44.195
A
A
26
27
14.950
A
A
36
35
3.562
11.129
0.058
-0.639
AA_U26U27:G35A36_AA
5
-3.255
4.373
42.720
-1.961
-0.402
3.219
31.280
A
A
27
28
0.792
A
A
35
34
3.227
0.425
0.340
-1.503
AA_U27C28:G34G35_AA
6
5.263
-9.806
30.842
-2.868
0.358
2.860
57.603
A
A
17
18
19.767
A
A
14
13
3.504
18.751
4.583
-2.086
AA_A17G18:C13G14_AA
7
1.998
-2.106
54.680
-3.180
-4.648
2.927
42.154
A
A
18
19
6.124
A
A
13
12
3.116
4.396
0.488
-1.545
AA_G18U19:G12C13_AA
8
-1.566
2.181
41.907
-2.568
-0.828
2.299
23.999
A
A
19
20
21.025
A
A
12
11
3.258
8.554
-0.793
-2.086
AA_U19C20:G11G12_AA
9
0.500
-1.229
22.438
-7.446
2.050
0.850
20.625
A
A
20
21
43.504
A
A
11
10
2.424
14.129
-1.416
-1.539
AA_C20G21:C10G11_AA
10
-2.038
6.275
14.925
-7.908
3.434
3.391
52.720
A
A
21
42
4.722
A
A
10
9
3.196
4.171
-1.472
0.083
AA_G21A42:U9C10_AA
11
-9.257
10.481
51.802
-0.182
1.046
3.442
28.377
A
A
42
43
12.238
A
A
9
8
3.709
5.925
0.122
-0.740
AA_A42U43:A8U9_AA
12
5.080
-10.493
27.304
-3.031
1.056
2.454
33.492
A
A
43
44
14.839
A
A
8
7
3.512
8.219
0.145
-2.468
AA_U43C44:G7A8_AA
13
-13.747
24.819
29.511
-5.602
-2.456
2.669
31.200
A
A
44
45
10.426
A
A
7
6
3.003
5.556
-0.111
-1.345
AA_C44U45:A6G7_AA
14
4.968
-9.322
30.318
-3.431
1.038
2.809
34.909
A
A
45
46
16.130
A
A
6
5
3.270
9.559
-0.517
-1.242
AA_U45G46:C5A6_AA
15
0.872
-1.471
33.603
-3.443
0.986
2.583
49.521
A
A
46
47
6.415
A
A
5
49
3.034
5.364
-0.555
-4.407
AA_G46U47:A49C5_AA
16
-1.239
1.482
49.233
-5.603
0.583
2.713
36.049
A
A
53
54
19.573
A
A
67
66
3.360
11.899
0.427
-1.490
AA_C53C54:G66G67_AA
17
0.601
-0.989
34.085
-4.022
-0.609
2.956
28.721
A
A
54
55
17.782
A
A
66
65
3.667
8.635
-0.689
-2.062
AA_C54C55:G65G66_AA
18
-5.490
11.306
26.873
-6.190
0.095
2.563
31.653
A
A
55
56
13.769
A
A
65
64
3.045
7.443
0.750
-1.791
AA_C55A56:U64G65_AA
19
0.463
-0.857
30.784
-4.479
-1.300
3.296
31.059
A
A
56
57
10.324
A
A
64
63
3.641
5.488
0.316
-1.751
AA_A56G57:C63U64_AA
20
3.677
-6.917
30.365
-4.401
0.166
3.025
64.072
A
A
57
58
4.252
A
A
63
62
3.057
4.508
-0.649
-0.597
AA_G57G58:A62C63_AA
21
-1.372
1.294
63.917
-0.743
0.557
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Data collection
Database references
Derived calculations
1
0
2014-04-30
1
1
2017-11-22
1
2
2024-02-28
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2014-03-04
REL
REL
MG
MAGNESIUM ION
HOH
water
RNA was prepared by in vitro transcription with T7 polymerase
11079
Murray Valley encephalitis virus
sample
MG
1
2
MG
MG
101
A
MG
1
2
MG
MG
102
A
MG
1
2
MG
MG
103
A
MG
1
2
MG
MG
104
A
MG
1
2
MG
MG
105
A
MG
1
2
MG
MG
106
A
MG
1
2
MG
MG
107
A
MG
1
2
MG
MG
108
A
MG
1
2
MG
MG
109
A
HOH
1
3
HOH
HOH
201
A
HOH
2
3
HOH
HOH
202
A
HOH
3
3
HOH
HOH
203
A
HOH
4
3
HOH
HOH
204
A
HOH
5
3
HOH
HOH
205
A
HOH
6
3
HOH
HOH
206
A
HOH
13
3
HOH
HOH
207
A
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
C
5
n
5
C
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
A
8
n
8
A
8
A
U
9
n
9
U
9
A
C
10
n
10
C
10
A
G
11
n
11
G
11
A
G
12
n
12
G
12
A
C
13
n
13
C
13
A
G
14
n
14
G
14
A
A
15
n
15
A
15
A
A
16
n
16
A
16
A
A
17
n
17
A
17
A
G
18
n
18
G
18
A
U
19
n
19
U
19
A
C
20
n
20
C
20
A
G
21
n
21
G
21
A
C
22
n
22
C
22
A
C
23
n
23
C
23
A
A
24
n
24
A
24
A
C
25
n
25
C
25
A
U
26
n
26
U
26
A
U
27
n
27
U
27
A
C
28
n
28
C
28
A
G
29
n
29
G
29
A
C
30
n
30
C
30
A
C
31
n
31
C
31
A
G
32
n
32
G
32
A
A
33
n
33
A
33
A
G
34
n
34
G
34
A
G
35
n
35
G
35
A
A
36
n
36
A
36
A
G
37
n
37
G
37
A
U
38
n
38
U
38
A
G
39
n
39
G
39
A
C
40
n
40
C
40
A
A
41
n
41
A
41
A
A
42
n
42
A
42
A
U
43
n
43
U
43
A
C
44
n
44
C
44
A
U
45
n
45
U
45
A
G
46
n
46
G
46
A
U
47
n
47
U
47
A
G
48
n
48
G
48
A
A
49
n
49
A
49
A
G
50
n
50
G
50
A
G
51
n
51
G
51
A
C
52
n
52
C
52
A
C
53
n
53
C
53
A
C
54
n
54
C
54
A
C
55
n
55
C
55
A
A
56
n
56
A
56
A
G
57
n
57
G
57
A
G
58
n
58
G
58
A
A
59
n
59
A
59
A
G
60
n
60
G
60
A
G
61
n
61
G
61
A
A
62
n
62
A
62
A
C
63
n
63
C
63
A
U
64
n
64
U
64
A
G
65
n
65
G
65
A
G
66
n
66
G
66
A
G
67
n
67
G
67
A
U
68
n
68
U
68
A
author_defined_assembly
1
monomeric
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
A
C
23
A
OP2
C
23
1_555
92.8
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
201
K
O
HOH
1_555
87.8
A
C
23
A
OP2
C
23
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
201
K
O
HOH
1_555
135.0
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
202
K
O
HOH
1_555
154.9
A
C
23
A
OP2
C
23
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
202
K
O
HOH
1_555
90.0
A
HOH
201
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
202
K
O
HOH
1_555
107.5
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
203
K
O
HOH
1_555
78.5
A
C
23
A
OP2
C
23
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
203
K
O
HOH
1_555
155.7
A
HOH
201
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
203
K
O
HOH
1_555
67.9
A
HOH
202
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
203
K
O
HOH
1_555
88.8
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
64.1
A
C
23
A
OP2
C
23
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
92.8
A
HOH
201
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
126.8
A
HOH
202
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
90.9
A
HOH
203
K
O
HOH
1_555
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
63.0
A
A
16
A
OP1
A
16
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
204
K
O
HOH
1_555
165.5
A
A
16
A
OP1
A
16
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
205
K
O
HOH
1_555
117.5
A
HOH
204
K
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
205
K
O
HOH
1_555
75.7
A
A
16
A
OP1
A
16
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
206
K
O
HOH
1_555
142.4
A
HOH
204
K
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
206
K
O
HOH
1_555
50.6
A
HOH
205
K
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
206
K
O
HOH
1_555
48.7
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
A
O
O
HOH
HOH
205
206
2.14
1
A
A
O
O
HOH
HOH
204
206
2.19
1
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N9
G
G
G
21
21
21
N
1
-2.47
0.40
120.30
117.83
A
A
A
C6
N1
C2
C
C
C
31
31
31
N
1
4.61
0.60
123.90
128.51
A
A
A
N1
C2
N3
G
G
G
32
32
32
N
1
-4.10
0.50
111.90
107.80
A
A
A
C2
N3
C4
G
G
G
32
32
32
N
1
-4.12
0.60
130.40
126.28
A
A
A
C6
C5
N7
G
G
G
32
32
32
N
1
-8.02
0.90
116.20
108.18
A
A
A
N1
C2
N2
G
G
G
32
32
32
N
1
-3.62
0.50
104.30
100.68
A
A
A
C5
N7
C8
G
G
G
48
48
48
N
1
4.23
0.50
113.10
117.33
A
A
A
N7
C8
N9
G
G
G
48
48
48
N
1
-4.48
0.40
106.40
101.92
A
A
A
C8
N9
C4
G
G
G
48
48
48
N
1
2.56
0.40
105.40
107.96
A
A
A
N9
C4
C5
G
G
G
48
48
48
N
0.2835
0.2303
0.2357
2.463
50.140
824
8418
9.91
85.47
0.35
RANDOM
1
1.39
SAD
38.25
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
2.463
50.140
7
1482
9
1466
0
0.006
1641
1.247
2560
14.545
813
0.050
340
0.007
68
0.6652
0.4780
2.5422
24
180
13.00
0.4572
0.4380
2.6331
63
611
40.00
0.3844
0.3632
2.7385
142
1344
91.00
0.3826
0.3357
2.8631
165
1450
100.00
0.3750
0.3115
3.0141
165
1495
100.00
0.2777
0.2623
3.2029
166
1478
100.00
0.2881
0.2303
3.4501
166
1483
100.00
0.2516
0.2166
3.7972
159
1507
100.00
0.2710
0.2010
4.3464
164
1481
100.00
0.2577
0.2051
5.4749
165
1510
100.00
0.2714
0.2051
50.1505
163
1477
99.00
2.45
50.14
4PQV
9499
1
2.45
1
data collection
Blu-Ice
Ice
model building
PHENIX
refinement
PHENIX
(phenix.refine: 1.8.4_1496)
data reduction
d*TREK
data scaling
d*TREK
phasing
PHENIX
Crystal structure of an Xrn1-resistant RNA from the 3' untranslated region of a flavivirus (Murray Valley Encephalitis virus)
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
metalc
2.215
A
C
5
A
OP2
C
5
1_555
A
MG
102
C
MG
MG
1_555
metalc
2.988
A
G
11
A
O6
G
11
1_555
A
MG
107
H
MG
MG
1_555
metalc
2.997
A
A
16
A
OP1
A
16
1_555
A
MG
104
E
MG
MG
1_555
metalc
1.776
A
C
23
A
OP2
C
23
1_555
A
MG
102
C
MG
MG
1_555
metalc
2.233
A
G
67
A
O6
G
67
1_555
A
MG
109
J
MG
MG
1_555
metalc
1.999
A
MG
102
C
MG
MG
1_555
A
HOH
201
K
O
HOH
1_555
metalc
2.088
A
MG
102
C
MG
MG
1_555
A
HOH
202
K
O
HOH
1_555
metalc
2.182
A
MG
102
C
MG
MG
1_555
A
HOH
203
K
O
HOH
1_555
metalc
2.225
A
MG
102
C
MG
MG
1_555
A
HOH
207
K
O
HOH
1_555
metalc
2.249
A
MG
104
E
MG
MG
1_555
A
HOH
204
K
O
HOH
1_555
metalc
2.354
A
MG
104
E
MG
MG
1_555
A
HOH
205
K
O
HOH
1_555
metalc
2.769
A
MG
104
E
MG
MG
1_555
A
HOH
206
K
O
HOH
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
40
A
N3
C
40
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
40
A
O2
C
40
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
40
A
N4
C
40
1_555
hydrog
HOOGSTEEN
A
U
4
A
N3
U
4
1_555
A
A
24
A
N7
A
24
1_555
hydrog
HOOGSTEEN
A
U
4
A
O4
U
4
1_555
A
A
24
A
N6
A
24
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
46
A
N1
G
46
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
46
A
O6
G
46
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
46
A
N2
G
46
1_555
hydrog
WATSON-CRICK
A
A
6
A
N1
A
6
1_555
A
U
45
A
N3
U
45
1_555
hydrog
WATSON-CRICK
A
A
6
A
N6
A
6
1_555
A
U
45
A
O4
U
45
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
A
C
44
A
N3
C
44
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
A
C
44
A
O2
C
44
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
A
C
44
A
N4
C
44
1_555
hydrog
WATSON-CRICK
A
A
8
A
N1
A
8
1_555
A
U
43
A
N3
U
43
1_555
hydrog
WATSON-CRICK
A
A
8
A
N6
A
8
1_555
A
U
43
A
O4
U
43
1_555
hydrog
WATSON-CRICK
A
U
9
A
N3
U
9
1_555
A
A
42
A
N1
A
42
1_555
hydrog
WATSON-CRICK
A
U
9
A
O4
U
9
1_555
A
A
42
A
N6
A
42
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
A
G
21
A
N1
G
21
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
A
G
21
A
O6
G
21
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
A
G
21
A
N2
G
21
1_555
hydrog
G-C PAIR
A
G
11
A
N1
G
11
1_555
A
C
20
A
N3
C
20
1_555
hydrog
TYPE_28_PAIR
A
G
12
A
N1
G
12
1_555
A
U
19
A
O2
U
19
1_555
hydrog
TYPE_28_PAIR
A
G
12
A
O6
G
12
1_555
A
U
19
A
N3
U
19
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
13
1_555
A
G
18
A
N1
G
18
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
13
1_555
A
G
18
A
O6
G
18
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
13
1_555
A
G
18
A
N2
G
18
1_555
hydrog
G-A MISPAIR
A
G
14
A
N2
G
14
1_555
A
A
17
A
N7
A
17
1_555
hydrog
WATSON-CRICK
A
C
23
A
N3
C
23
1_555
A
G
39
A
N1
G
39
1_555
hydrog
WATSON-CRICK
A
C
23
A
N4
C
23
1_555
A
G
39
A
O6
G
39
1_555
hydrog
WATSON-CRICK
A
C
23
A
O2
C
23
1_555
A
G
39
A
N2
G
39
1_555
hydrog
WATSON-CRICK
A
C
25
A
N3
C
25
1_555
A
G
37
A
N1
G
37
1_555
hydrog
WATSON-CRICK
A
C
25
A
N4
C
25
1_555
A
G
37
A
O6
G
37
1_555
hydrog
WATSON-CRICK
A
C
25
A
O2
C
25
1_555
A
G
37
A
N2
G
37
1_555
hydrog
WATSON-CRICK
A
U
26
A
N3
U
26
1_555
A
A
36
A
N1
A
36
1_555
hydrog
WATSON-CRICK
A
U
26
A
O4
U
26
1_555
A
A
36
A
N6
A
36
1_555
hydrog
TYPE_28_PAIR
A
U
27
A
N3
U
27
1_555
A
G
35
A
O6
G
35
1_555
hydrog
TYPE_28_PAIR
A
U
27
A
O2
U
27
1_555
A
G
35
A
N1
G
35
1_555
hydrog
WATSON-CRICK
A
C
28
A
N3
C
28
1_555
A
G
34
A
N1
G
34
1_555
hydrog
WATSON-CRICK
A
C
28
A
N4
C
28
1_555
A
G
34
A
O6
G
34
1_555
hydrog
WATSON-CRICK
A
C
28
A
O2
C
28
1_555
A
G
34
A
N2
G
34
1_555
hydrog
HOOGSTEEN
A
U
47
A
N3
U
47
1_555
A
A
49
A
N7
A
49
1_555
hydrog
HOOGSTEEN
A
U
47
A
O4
U
47
1_555
A
A
49
A
N6
A
49
1_555
hydrog
WATSON-CRICK
A
C
53
A
N3
C
53
1_555
A
G
67
A
N1
G
67
1_555
hydrog
WATSON-CRICK
A
C
53
A
N4
C
53
1_555
A
G
67
A
O6
G
67
1_555
hydrog
WATSON-CRICK
A
C
53
A
O2
C
53
1_555
A
G
67
A
N2
G
67
1_555
hydrog
WATSON-CRICK
A
C
54
A
N3
C
54
1_555
A
G
66
A
N1
G
66
1_555
hydrog
WATSON-CRICK
A
C
54
A
N4
C
54
1_555
A
G
66
A
O6
G
66
1_555
hydrog
WATSON-CRICK
A
C
54
A
O2
C
54
1_555
A
G
66
A
N2
G
66
1_555
hydrog
WATSON-CRICK
A
C
55
A
N3
C
55
1_555
A
G
65
A
N1
G
65
1_555
hydrog
WATSON-CRICK
A
C
55
A
N4
C
55
1_555
A
G
65
A
O6
G
65
1_555
hydrog
WATSON-CRICK
A
C
55
A
O2
C
55
1_555
A
G
65
A
N2
G
65
1_555
hydrog
WATSON-CRICK
A
A
56
A
N1
A
56
1_555
A
U
64
A
N3
U
64
1_555
hydrog
WATSON-CRICK
A
A
56
A
N6
A
56
1_555
A
U
64
A
O4
U
64
1_555
hydrog
WATSON-CRICK
A
G
57
A
N1
G
57
1_555
A
C
63
A
N3
C
63
1_555
hydrog
WATSON-CRICK
A
G
57
A
N2
G
57
1_555
A
C
63
A
O2
C
63
1_555
hydrog
WATSON-CRICK
A
G
57
A
O6
G
57
1_555
A
C
63
A
N4
C
63
1_555
hydrog
TYPE_11_PAIR
A
G
58
A
N2
G
58
1_555
A
A
62
A
N7
A
62
1_555
hydrog
TYPE_11_PAIR
A
G
58
A
N3
G
58
1_555
A
A
62
A
N6
A
62
1_555
hydrog
G-U MISPAIR
A
G
66
A
N2
G
66
1_555
A
U
68
A
O4
U
68
1_555
RNA
flavivirus, 3' untranslated region, sfRNA, pseudoknot, Type C RNA three-way junction, Xrn1 resistant RNA, xrRNA), resists degradation, exonuclease Xrn1, small flaviviral RNA, RNA
KC852196.1
GB
1
10594
KC852196.1
GUGUCAGAUCGCGAAAGCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU
10594
10659
4PQV
1
68
KC852196.1
A
1
1
68
1
U
engineered mutation
G
2
4PQV
A
KC852196.1
GB
10595
2
1
insertion
G
11
4PQV
A
KC852196.1
GB
11
1
insertion
U
19
4PQV
A
KC852196.1
GB
19
BINDING SITE FOR RESIDUE MG A 102
A
MG
102
Software
6
BINDING SITE FOR RESIDUE MG A 103
A
MG
103
Software
1
BINDING SITE FOR RESIDUE MG A 104
A
MG
104
Software
6
BINDING SITE FOR RESIDUE MG A 105
A
MG
105
Software
1
BINDING SITE FOR RESIDUE MG A 107
A
MG
107
Software
1
BINDING SITE FOR RESIDUE MG A 108
A
MG
108
Software
1
BINDING SITE FOR RESIDUE MG A 109
A
MG
109
Software
2
A
C
5
A
C
5
6
1_555
A
C
23
A
C
23
6
1_555
A
HOH
201
K
HOH
6
1_555
A
HOH
202
K
HOH
6
1_555
A
HOH
203
K
HOH
6
1_555
A
HOH
207
K
HOH
6
1_555
A
G
51
A
G
51
1
1_555
A
G
14
A
G
14
6
1_555
A
A
16
A
A
16
6
1_555
A
G
58
A
G
58
6
5_565
A
HOH
204
K
HOH
6
1_555
A
HOH
205
K
HOH
6
1_555
A
HOH
206
K
HOH
6
1_555
A
G
58
A
G
58
1
1_555
A
G
11
A
G
11
1
1_555
A
A
59
A
A
59
1
5_565
A
G
66
A
G
66
2
1_555
A
G
67
A
G
67
2
1_555
154
P 32 2 1