1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Klinck, R.
Westhof, E.
Walker, S.
Afshar, M.
Collier, A.
Aboul-ela, F.
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
UK
RNA
RNARFU
2122
1355-8382
6
1423
1431
10.1017/S1355838200000935
11073218
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
2000
10.2210/pdb1fqz/pdb
pdb_00001fqz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8800.279
HEPATITIS C VIRUS IRES DOMAIN IIID
1
syn
polymer
no
no
GCCGAGUAGUGUUGGGUCGCGAAAGGC
GCCGAGUAGUGUUGGGUCGCGAAAGGC
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
9.480
1
19
A
1
A
27
-7.037
A_G1:C27_A
1
-2.036
-1.132
0.013
-0.210
9.805
1
19
A
2
A
26
0.268
A_C2:G26_A
2
-12.096
1.244
-0.332
-0.167
-3.774
1
19
A
3
A
25
-1.699
A_C3:G25_A
3
-12.708
1.083
-0.282
-0.236
-2.074
10
11
A
4
A
24
-7.827
A_G4:A24_A
4
-8.198
7.022
0.002
-4.575
-15.371
8
2
A
5
A
23
-174.790
A_A5:A23_A
5
2.911
-6.412
0.007
5.484
15.454
4
24
A
7
A
22
-105.743
A_U7:A22_A
6
-30.792
4.142
-1.508
-1.338
-3.784
10
11
A
8
A
21
-6.783
A_A8:G21_A
7
3.136
-7.026
-0.355
-4.316
-3.117
1
19
A
9
A
20
-5.884
A_G9:C20_A
8
-5.484
-0.763
-0.467
-0.109
-6.290
28
A
10
A
19
-12.489
A_U10:G19_A
9
-4.434
1.828
-0.089
-0.398
-4.069
1
19
A
11
A
18
-11.009
A_G11:C18_A
10
-11.327
-0.368
0.403
-0.106
-13.522
27
A
12
A
16
-159.547
A_U12:G16_A
11
-1.044
-0.270
-0.150
1.318
3.142
44.301
A
A
1
2
4.172
A
A
27
26
3.233
3.143
0.199
-1.311
AA_G1C2:G26C27_AA
1
1.594
-2.116
44.167
-2.024
-0.119
2.845
32.555
A
A
2
3
16.539
A
A
26
25
3.503
9.141
0.155
-1.911
AA_C2C3:G25G26_AA
2
2.973
-5.379
31.141
-4.992
0.238
3.213
59.763
A
A
3
4
6.860
A
A
25
24
3.404
6.814
-0.195
-1.348
AA_C3G4:A24G25_AA
3
6.120
-6.162
59.121
-1.699
0.507
0.070
178.611
A
A
4
5
75.356
A
A
24
23
0.704
150.507
-3.624
0.114
AA_G4A5:A23A24_AA
4
90.924
-45.524
140.985
0.000
1.847
0.510
-175.965
A
A
5
7
-64.238
A
A
23
22
0.851
127.759
2.589
-1.560
AA_A5U7:A22A23_AA
5
113.725
57.181
-126.399
0.660
1.403
4.136
-6.562
A
A
7
8
-22.556
A
A
22
21
3.758
2.515
5.559
-0.998
AA_U7A8:G21A22_AA
6
-0.340
-3.054
-6.052
-5.016
46.706
3.315
62.325
A
A
8
9
4.724
A
A
21
20
3.427
4.884
0.257
-1.310
AA_A8G9:C20G21_AA
7
-2.454
2.373
62.109
-1.496
-0.364
3.218
41.482
A
A
9
10
5.469
A
A
20
19
3.372
3.868
-0.442
-1.696
AA_G9U10:G19C20_AA
8
-1.144
1.618
41.294
-2.811
0.501
2.930
26.791
A
A
10
11
7.282
A
A
19
18
3.173
3.365
0.120
-1.790
AA_U10G11:C18G19_AA
9
0.807
-1.747
26.571
-4.678
-0.063
3.171
92.942
A
A
11
12
-2.642
A
A
18
16
3.206
-3.830
-1.175
-0.483
AA_G11U12:G16C18_AA
10
4.742
-3.272
92.788
-0.263
0.897
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-01-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2000-09-07
REL
Transcribed using T7 RNA polymerase
sample
structures with acceptable covalent geometry, structures with favorable non-bond energy
1
1
2D NOESY
2D NOESY
2D NOESY
2D NOESY
8mM Na phosphate
6.6
ambient
278
K
8mM Na phosphate
6.6
ambient
298
K
8mM Na phosphate
6.6
ambient
303
K
Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually.
Using a motif-based approach, a model was constructed from X-ray and NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data.
1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6
90% H2O/10% D2O
1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6
100% D2O
Bruker
collection
XwinNMR
2.5
Delaglio
processing
NMRPipe
1.7
Goddard & Kneller
data analysis
Sparky
3.66
Brooks et al.
refinement
CHARMM
25.2
MSI
refinement
Insight II
97.0
500
Bruker
DRX
600
Bruker
DMX
G
1
n
1
G
1
A
C
2
n
2
C
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
G
6
n
6
G
6
A
U
7
n
7
U
7
A
A
8
n
8
A
8
A
G
9
n
9
G
9
A
U
10
n
10
U
10
A
G
11
n
11
G
11
A
U
12
n
12
U
12
A
U
13
n
13
U
13
A
G
14
n
14
G
14
A
G
15
n
15
G
15
A
G
16
n
16
G
16
A
U
17
n
17
U
17
A
C
18
n
18
C
18
A
G
19
n
19
G
19
A
C
20
n
20
C
20
A
G
21
n
21
G
21
A
A
22
n
22
A
22
A
A
23
n
23
A
23
A
A
24
n
24
A
24
A
G
25
n
25
G
25
A
G
26
n
26
G
26
A
C
27
n
27
C
27
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
1
A
U
12
0.075
SIDE CHAIN
1
6.43
0.70
119.90
126.33
A
A
A
N3
C2
N2
G
G
G
1
1
1
N
1
3.73
0.60
119.90
123.63
A
A
A
N1
C6
O6
G
G
G
1
1
1
N
1
4.45
0.70
108.50
112.95
A
A
A
O4'
C1'
N1
C
C
C
3
3
3
N
1
6.72
0.70
119.90
126.62
A
A
A
N3
C2
N2
G
G
G
4
4
4
N
1
6.67
0.60
118.60
125.27
A
A
A
N1
C6
N6
A
A
A
5
5
5
N
1
5.54
0.70
119.90
125.44
A
A
A
N3
C2
N2
G
G
G
6
6
6
N
1
6.64
0.60
118.60
125.24
A
A
A
N1
C6
N6
A
A
A
8
8
8
N
1
6.39
0.70
119.90
126.29
A
A
A
N3
C2
N2
G
G
G
9
9
9
N
1
6.76
0.70
119.90
126.66
A
A
A
N3
C2
N2
G
G
G
11
11
11
N
1
3.79
0.60
119.90
123.69
A
A
A
N1
C6
O6
G
G
G
11
11
11
N
1
-3.61
0.60
128.60
124.99
A
A
A
C5
C6
O6
G
G
G
11
11
11
N
1
4.31
0.70
108.50
112.81
A
A
A
O4'
C1'
N1
U
U
U
12
12
12
N
1
6.22
0.70
119.90
126.12
A
A
A
N3
C2
N2
G
G
G
14
14
14
N
1
6.18
0.70
119.90
126.08
A
A
A
N3
C2
N2
G
G
G
15
15
15
N
1
3.63
0.60
119.90
123.53
A
A
A
N1
C6
O6
G
G
G
15
15
15
N
1
6.53
0.70
119.90
126.43
A
A
A
N3
C2
N2
G
G
G
16
16
16
N
1
3.92
0.60
119.90
123.82
A
A
A
N1
C6
O6
G
G
G
16
16
16
N
1
-3.67
0.60
128.60
124.93
A
A
A
C5
C6
O6
G
G
G
16
16
16
N
1
6.49
0.70
119.90
126.39
A
A
A
N3
C2
N2
G
G
G
19
19
19
N
1
3.83
0.60
119.90
123.73
A
A
A
N1
C6
O6
G
G
G
19
19
19
N
1
-3.76
0.60
128.60
124.84
A
A
A
C5
C6
O6
G
G
G
19
19
19
N
1
4.42
0.70
108.50
112.92
A
A
A
O4'
C1'
N1
C
C
C
20
20
20
N
1
6.98
0.70
119.90
126.88
A
A
A
N3
C2
N2
G
G
G
21
21
21
N
1
3.62
0.60
119.90
123.52
A
A
A
N1
C6
O6
G
G
G
21
21
21
N
1
6.63
0.60
118.60
125.23
A
A
A
N1
C6
N6
A
A
A
22
22
22
N
1
6.92
0.60
118.60
125.52
A
A
A
N1
C6
N6
A
A
A
23
23
23
N
1
6.87
0.60
118.60
125.47
A
A
A
N1
C6
N6
A
A
A
24
24
24
N
1
6.17
0.70
119.90
126.07
A
A
A
N3
C2
N2
G
G
G
25
25
25
N
1
3.70
0.60
119.90
123.60
A
A
A
N1
C6
O6
G
G
G
25
25
25
N
1
6.09
0.70
119.90
125.99
A
A
A
N3
C2
N2
G
G
G
26
26
26
N
1
3.63
0.60
119.90
123.53
A
A
A
N1
C6
O6
G
G
G
26
26
26
N
1
A
A
C2
N3
U
U
7
7
0.042
0.007
1.373
1.415
N
1
A
A
C2
N3
U
U
10
10
0.045
0.007
1.373
1.418
N
1
A
A
C2
N3
U
U
13
13
0.046
0.007
1.373
1.419
N
1
A
A
C2
N3
U
U
17
17
0.046
0.007
1.373
1.419
N
NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
A
G
26
A
N1
G
26
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
A
G
26
A
O6
G
26
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
A
G
26
A
N2
G
26
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
25
A
N1
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
25
A
O6
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
25
A
N2
G
25
1_555
hydrog
TYPE_11_PAIR
A
G
4
A
N2
G
4
1_555
A
A
24
A
N7
A
24
1_555
hydrog
TYPE_11_PAIR
A
G
4
A
N3
G
4
1_555
A
A
24
A
N6
A
24
1_555
hydrog
TYPE_2_PAIR
A
A
5
A
N6
A
5
1_555
A
A
23
A
N7
A
23
1_555
hydrog
TYPE_2_PAIR
A
A
5
A
N7
A
5
1_555
A
A
23
A
N6
A
23
1_555
hydrog
G-U MISPAIR
A
G
6
A
N2
G
6
1_555
A
U
7
A
O4
U
7
1_555
hydrog
REVERSED HOOGSTEEN
A
U
7
A
N3
U
7
1_555
A
A
22
A
N7
A
22
1_555
hydrog
REVERSED HOOGSTEEN
A
U
7
A
O2
U
7
1_555
A
A
22
A
N6
A
22
1_555
hydrog
TYPE_11_PAIR
A
A
8
A
N6
A
8
1_555
A
G
21
A
N3
G
21
1_555
hydrog
TYPE_11_PAIR
A
A
8
A
N7
A
8
1_555
A
G
21
A
N2
G
21
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
20
A
N3
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
20
A
O2
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
20
A
N4
C
20
1_555
hydrog
TYPE_28_PAIR
A
U
10
A
N3
U
10
1_555
A
G
19
A
O6
G
19
1_555
hydrog
TYPE_28_PAIR
A
U
10
A
O2
U
10
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
A
C
18
A
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
A
C
18
A
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
A
C
18
A
N4
C
18
1_555
hydrog
TYPE_27_PAIR
A
U
12
A
N3
U
12
1_555
A
G
16
A
O6
G
16
1_555
hydrog
TYPE_27_PAIR
A
U
12
A
O4
U
12
1_555
A
G
16
A
N1
G
16
1_555
RNA
trans wobble G.U pair, S-turn, sarcin-ricin loop, loop E motif, sheared G.A pair, reverse Hoogsteen A.U pair, RNA
1FQZ
PDB
1
1FQZ
1
27
1FQZ
1
27
1FQZ
A
1
1
27
1
P 1