1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lukavsky, P.J.
Otto, G.A.
Lancaster, A.M.
Sarnow, P.
Puglisi, J.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
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
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
doub
N
119
N
sing
N
120
N
sing
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
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
7
1105
1110
10.1038/81951
11101890
Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function.
2000
10.2210/pdb1f84/pdb
pdb_00001f84
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9450.667
HCV-1B IRES RNA DOMAIN IIID
HCV IRES RNA DOMAIN IIID (NUCLEOTIDES 252-290 OF GENOMIC HEPATITIS C VIRAL RNA)
A252G
1
syn
polymer
no
no
GGCCGAGUAGUGUUGGGUCGCGAAAGGCC
GGCCGAGUAGUGUUGGGUCGCGAAAGGCC
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
-0.191
1
19
A
2
A
28
-4.230
A_G2:C28_A
1
-25.787
0.295
0.411
-0.312
2.628
1
19
A
3
A
27
-3.312
A_C3:G27_A
2
-24.032
-0.451
0.481
-0.177
-0.735
1
19
A
4
A
26
-0.306
A_C4:G26_A
3
-30.035
-0.103
-0.307
-0.303
0.201
10
A
5
A
25
-15.806
A_G5:A25_A
4
-16.574
6.777
0.320
-5.786
11.989
8
2
A
6
A
24
179.451
A_A6:A24_A
5
-2.356
5.506
-0.414
-5.263
20.493
4
24
A
8
A
23
-104.471
A_U8:A23_A
6
-15.529
3.558
-0.759
-1.258
-0.341
9
11
A
9
A
22
-5.326
A_A9:G22_A
7
-3.235
-6.405
-0.563
-4.160
-15.161
1
19
A
10
A
21
2.045
A_G10:C21_A
8
-21.178
-0.001
-0.690
-0.357
-20.178
1
28
A
11
A
20
-4.911
A_U11:G20_A
9
-22.682
1.617
0.691
-0.460
-26.056
1
19
A
12
A
19
-14.342
A_G12:C19_A
10
5.941
0.738
-2.032
-0.578
49.885
A
14
A
17
-89.389
A_U14:G17_A
11
26.509
-0.946
0.694
-7.229
3.264
30.487
A
A
2
3
-13.288
A
A
28
27
2.914
-6.929
0.167
-1.912
AA_G2C3:G27C28_AA
1
-0.281
0.539
29.706
-2.315
-0.371
2.822
35.541
A
A
3
4
14.775
A
A
27
26
3.167
8.904
-0.284
-0.769
AA_C3C4:G26G27_AA
2
4.675
-7.758
34.133
-2.475
1.104
3.403
72.367
A
A
4
5
7.570
A
A
26
25
3.453
8.921
-0.741
-0.299
AA_C4G5:A25G26_AA
3
-0.175
0.148
71.890
-0.563
0.621
2.395
-175.787
A
A
5
6
-47.223
A
A
25
24
1.687
92.607
0.152
-3.774
AA_G5A6:A24A25_AA
4
-149.328
-76.148
-21.387
0.996
-1.362
1.020
174.166
A
A
6
8
54.643
A
A
24
23
1.106
107.867
1.444
2.258
AA_A6U8:A23A24_AA
5
-133.118
67.435
95.303
0.871
-1.043
-3.957
9.137
A
A
8
9
45.257
A
A
23
22
3.476
5.280
4.982
-1.592
AA_U8A9:G22A23_AA
6
-7.120
61.027
2.218
-8.592
-29.378
3.827
64.278
A
A
9
10
5.008
A
A
22
21
3.884
5.322
0.621
-0.918
AA_A9G10:C21G22_AA
7
2.853
-2.685
64.024
-1.132
-0.440
3.777
44.316
A
A
10
11
-16.666
A
A
21
20
3.644
-12.379
-0.509
-0.865
AA_G10U11:G20C21_AA
8
-6.345
8.542
42.181
0.195
-0.013
2.879
34.685
A
A
11
12
9.454
A
A
20
19
3.698
5.442
-0.305
-2.029
AA_U11G12:C19G20_AA
9
14.768
-25.657
31.006
-4.294
2.927
4.723
134.941
A
A
12
14
14.543
A
A
19
17
4.476
26.802
3.487
0.370
AA_G12U14:G17C19_AA
10
18.766
-10.183
132.927
-0.049
-1.713
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2000-11-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2000-06-28
REL
REL
Synthesized enzymatically in-vitro using T7 RNA Polymerase
sample
THE STRUCTURE WAS DETERMINED USING TRIPLE
RESONANCE HCN AND HCP EXPERIMENTS ON N15,C13-LABELLED RNA
structures with the least restraint violations,structures with the lowest energy
100
25
P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY
P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY
3D HCP, 3D HMQC-TOCSY, 3D C13-edited NOESY
10mM
6.40
ambient
283
K
10mM
6.40
ambient
298
K
SEE REFERENCE ABOVE
Simulated annealing and restrained molecular dynamics
21
closest to the average
1.5mM RNA, non-isotopically labelled
10mM sodium phosphate buffer, pH 6.40
96% H2O, 4% D2O or 100% D2O
1mM RNA, U-15N,13C
10mM sodium phosphate buffer, pH 6.40
96% H2O, 4% D2O or 100% D2O
Brunger
refinement
X-PLOR
3.1
Goddard
data analysis
Sparky
3.8
500
Varian
INOVA
800
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
C
4
n
4
C
4
A
G
5
n
5
G
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
U
8
n
8
U
8
A
A
9
n
9
A
9
A
G
10
n
10
G
10
A
U
11
n
11
U
11
A
G
12
n
12
G
12
A
U
13
n
13
U
13
A
U
14
n
14
U
14
A
G
15
n
15
G
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
U
18
n
18
U
18
A
C
19
n
19
C
19
A
G
20
n
20
G
20
A
C
21
n
21
C
21
A
G
22
n
22
G
22
A
A
23
n
23
A
23
A
A
24
n
24
A
24
A
A
25
n
25
A
25
A
G
26
n
26
G
26
A
G
27
n
27
G
27
A
C
28
n
28
C
28
A
C
29
n
29
C
29
A
author_defined_assembly
1
monomeric
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
5
A
A
HO2'
O6
G
G
7
22
1.52
18
A
A
H41
O6
C
G
4
26
1.56
15
24.23
1.90
111.70
135.93
A
A
A
O5'
C5'
C4'
G
G
G
1
1
1
N
15
A
A
O5'
C5'
G
G
1
1
-0.699
0.009
1.420
0.721
N
SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID
1
N
N
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
28
A
N3
C
28
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
28
A
O2
C
28
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
28
A
N4
C
28
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
27
A
N1
G
27
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
27
A
O6
G
27
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
27
A
N2
G
27
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
26
A
N1
G
26
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
26
A
O6
G
26
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
26
A
N2
G
26
1_555
hydrog
G-A MISPAIR
A
G
5
A
N2
G
5
1_555
A
A
25
A
N7
A
25
1_555
hydrog
A-G MISPAIR
A
A
6
A
N1
A
6
1_555
A
G
7
A
N2
G
7
1_555
hydrog
TYPE_2_PAIR
A
A
6
A
N6
A
6
1_555
A
A
24
A
N7
A
24
1_555
hydrog
TYPE_2_PAIR
A
A
6
A
N7
A
6
1_555
A
A
24
A
N6
A
24
1_555
hydrog
G-U MISPAIR
A
G
7
A
N2
G
7
1_555
A
U
8
A
O4
U
8
1_555
hydrog
REVERSED HOOGSTEEN
A
U
8
A
N3
U
8
1_555
A
A
23
A
N7
A
23
1_555
hydrog
REVERSED HOOGSTEEN
A
U
8
A
O2
U
8
1_555
A
A
23
A
N6
A
23
1_555
hydrog
TYPE_11_PAIR
A
A
9
A
N6
A
9
1_555
A
G
22
A
N3
G
22
1_555
hydrog
TYPE_11_PAIR
A
A
9
A
N7
A
9
1_555
A
G
22
A
N2
G
22
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
21
A
N4
C
21
1_555
hydrog
TYPE_28_PAIR
A
U
11
A
N3
U
11
1_555
A
G
20
A
O6
G
20
1_555
hydrog
TYPE_28_PAIR
A
U
11
A
O2
U
11
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
G
12
A
N1
G
12
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
12
A
N2
G
12
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
12
A
O6
G
12
1_555
A
C
19
A
N4
C
19
1_555
hydrog
U-G MISPAIR
A
U
14
A
O2
U
14
1_555
A
G
17
A
N2
G
17
1_555
RNA
Ribonucleic Acid, Hepatitis C virus internal ribosome entry site, Sarcin/Ricin loop, Loop E motif, Hairpin loop, RNA structure, RNA
1F84
PDB
1
1F84
1
29
1F84
1
29
1F84
A
1
1
29
1
P 1