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.
Kim, I.
Otto, G.A.
Puglisi, J.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
10
1033
1038
10.1038/nsb1004
14578934
Structure of HCV IRES domain II determined by NMR.
2003
10.2210/pdb1p5n/pdb
pdb_00001p5n
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
10970.565
34-MER
HCV IRES domain IIa (residues 69-98)
1
syn
polymer
no
no
GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC
GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC
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
28.061
1
19
A
1
A
34
18.413
A_G1:C34_A
1
-25.618
0.107
-0.608
-0.351
2.527
1
19
A
2
A
33
9.576
A_G2:C33_A
2
-22.536
0.239
-0.528
-0.110
19.075
1
19
A
3
A
32
4.161
A_C3:G32_A
3
-28.690
-0.038
-1.034
-0.191
-37.722
1
20
A
4
A
31
-6.450
A_A4:U31_A
4
-0.430
0.392
-1.420
0.163
-0.429
9
11
A
5
A
30
-5.701
A_G5:A30_A
5
9.448
6.503
-0.911
-3.229
0.468
4
24
A
6
A
29
-109.859
A_A6:U29_A
6
-16.713
-4.043
-0.941
-1.469
-19.135
8
2
A
7
A
27
-177.190
A_A7:A27_A
7
-10.294
-5.569
0.681
4.838
18.339
5
A
8
A
26
11.387
A_A8:U26_A
8
-18.698
-7.110
-0.084
-4.101
10.412
28
A
9
A
25
9.447
A_G9:U25_A
9
-32.654
-2.281
-0.140
-0.389
13.838
1
19
A
10
A
24
6.623
A_C10:G24_A
10
-32.665
-0.117
-0.485
-0.119
-3.816
1
19
A
11
A
23
-2.802
A_G11:C23_A
11
-21.733
0.258
-0.130
-0.292
4.348
28
A
12
A
22
-8.860
A_U12:G22_A
12
-20.345
1.472
-0.471
-0.434
2.211
1
19
A
13
A
21
-2.538
A_C13:G21_A
13
0.466
-0.417
-0.102
-0.094
2.599
36.867
A
A
1
2
41.913
A
A
34
33
3.858
24.374
-0.382
-0.545
AA_G1G2:C33C34_AA
1
-1.980
3.405
27.802
-4.621
0.299
2.562
33.556
A
A
2
3
3.075
A
A
33
32
2.641
1.771
-0.218
-0.717
AA_G2C3:G32C33_AA
2
3.704
-6.431
33.311
-1.474
0.863
2.609
38.336
A
A
3
4
41.150
A
A
32
31
5.132
24.951
0.122
-2.111
AA_C3A4:U31G32_AA
3
-1.048
1.728
29.320
-7.452
-0.364
2.292
61.463
A
A
4
5
-3.153
A
A
31
30
2.274
-3.220
-0.369
-0.169
AA_A4G5:A30U31_AA
4
-2.662
2.606
61.334
-0.060
0.274
2.563
-14.395
A
A
5
6
-67.232
A
A
30
29
3.251
13.267
-4.654
-1.344
AA_G5A6:U29A30_AA
5
0.183
0.927
-5.595
-10.016
-18.361
2.704
87.261
A
A
6
7
-6.525
A
A
29
27
2.702
-8.991
1.659
-1.190
AA_A6A7:A27U29_AA
6
-5.479
3.977
86.751
-0.700
-1.301
2.736
-59.744
A
A
7
8
-5.652
A
A
27
26
2.820
5.623
-0.821
0.981
AA_A7A8:U26A27_AA
7
0.781
0.785
-59.499
-1.224
-0.791
3.466
58.407
A
A
8
9
8.022
A
A
26
25
3.485
7.795
0.041
0.249
AA_A8G9:U25U26_AA
8
-6.655
6.850
57.579
-0.182
-0.415
3.224
44.542
A
A
9
10
-6.304
A
A
25
24
3.181
-4.770
-0.219
-0.578
AA_G9C10:G24U25_AA
9
-0.109
0.143
44.299
-0.331
0.280
3.064
38.075
A
A
10
11
30.368
A
A
24
23
3.715
18.943
-0.864
-0.527
AA_C10G11:C23G24_AA
10
-4.212
6.752
32.917
-3.498
0.727
2.811
41.630
A
A
11
12
-1.433
A
A
23
22
2.801
-1.018
-0.245
-1.133
AA_G11U12:G22C23_AA
11
2.240
-3.154
41.561
-1.501
0.548
3.489
28.661
A
A
12
13
-2.132
A
A
22
21
3.450
-1.055
0.879
-1.614
AA_U12C13:G21G22_AA
12
-0.562
1.135
28.637
-3.009
-1.910
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
2003-11-04
1
1
2008-04-29
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
2003-04-27
REL
REL
Synthesized by in vitro transcription from linearized plasmid DNA using T7 RNA polymerase
sample
The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings
lowest restraint violation and total energy
100
20
2D S-NOESY
2D NOESY
DQF-COSY
2D HP-COSY
3D_13C-separated_NOESY
3D HCP
3D HMQC TOCSY
10mM posphate buffer
6.40
ambient
288
K
10mM posphate buffer
6.40
ambient
298
K
10mM posphate buffer
6.40
ambient
303
K
see reference above
see reference above
1
minimized average structure
1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer
96% D2O, 4% H2O
1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer
100% D2O
1-2mM HCV IRES domain IIb RNA
U-15N,13C
10mM phosphate buffer
96% D2O, 4% H2O
1-2mM HCV IRES domain IIb RNA
U-15N,13C
10mM phosphate buffer
100% D2O
Varian
processing
VNMR
6.1C
Goddard, T.D. & Kneller D.G.
data analysis
Sparky
3
Brunger, A.T.
refinement
X-PLOR
3.1
Brunger, A.T.
refinement
CNS
1.1
Zweckstetter, M. & Bax, A.
refinement
PALES
1
500
Varian
INOVA
800
Varian
INOVA
GUA
1
n
1
G
1
A
GUA
2
n
2
G
2
A
CYT
3
n
3
C
3
A
ADE
4
n
4
A
4
A
GUA
5
n
5
G
5
A
ADE
6
n
6
A
6
A
ADE
7
n
7
A
7
A
ADE
8
n
8
A
8
A
GUA
9
n
9
G
9
A
CYT
10
n
10
C
10
A
GUA
11
n
11
G
11
A
URI
12
n
12
U
12
A
CYT
13
n
13
C
13
A
URI
14
n
14
U
14
A
ADE
15
n
15
A
15
A
GUA
16
n
16
G
16
A
CYT
17
n
17
C
17
A
CYT
18
n
18
C
18
A
ADE
19
n
19
A
19
A
URI
20
n
20
U
20
A
GUA
21
n
21
G
21
A
GUA
22
n
22
G
22
A
CYT
23
n
23
C
23
A
GUA
24
n
24
G
24
A
URI
25
n
25
U
25
A
URI
26
n
26
U
26
A
ADE
27
n
27
A
27
A
GUA
28
n
28
G
28
A
URI
29
n
29
U
29
A
ADE
30
n
30
A
30
A
URI
31
n
31
U
31
A
GUA
32
n
32
G
32
A
CYT
33
n
33
C
33
A
CYT
34
n
34
C
34
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
A
O6
HO2'
G
G
5
28
1.59
3
A
A
O2'
H8
U
G
20
21
1.57
4
A
A
O6
HO2'
G
G
5
28
1.60
8
A
A
O6
HO2'
G
G
5
28
1.59
9
A
A
O6
HO2'
G
G
5
28
1.57
10
A
A
H61
O2'
A
U
8
26
1.60
11
A
A
O6
HO2'
G
G
5
28
1.58
13
A
A
O2'
H8
U
G
20
21
1.59
15
A
A
O6
HO2'
G
G
5
28
1.56
15
A
A
H61
O2'
A
U
8
26
1.58
minimized average
Solution Structure of HCV IRES Domain IIb
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
34
A
N3
C
34
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
34
A
O2
C
34
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
34
A
N4
C
34
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
33
A
N3
C
33
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
33
A
O2
C
33
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
33
A
N4
C
33
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
32
A
N1
G
32
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
32
A
O6
G
32
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
32
A
N2
G
32
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
A
U
31
A
N3
U
31
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
A
U
31
A
O4
U
31
1_555
hydrog
TYPE_11_PAIR
A
G
5
A
N2
G
5
1_555
A
A
30
A
N7
A
30
1_555
hydrog
TYPE_11_PAIR
A
G
5
A
N3
G
5
1_555
A
A
30
A
N6
A
30
1_555
hydrog
G-U MISPAIR
A
G
5
A
N2
G
5
1_555
A
U
31
A
O4
U
31
1_555
hydrog
REVERSED HOOGSTEEN
A
A
6
A
N6
A
6
1_555
A
U
29
A
O2
U
29
1_555
hydrog
REVERSED HOOGSTEEN
A
A
6
A
N7
A
6
1_555
A
U
29
A
N3
U
29
1_555
hydrog
TYPE_2_PAIR
A
A
7
A
N6
A
7
1_555
A
A
27
A
N7
A
27
1_555
hydrog
TYPE_2_PAIR
A
A
7
A
N7
A
7
1_555
A
A
27
A
N6
A
27
1_555
hydrog
A-U PAIR
A
A
8
A
N6
A
8
1_555
A
U
26
A
O2
U
26
1_555
hydrog
TYPE_28_PAIR
A
G
9
A
N1
G
9
1_555
A
U
25
A
O2
U
25
1_555
hydrog
TYPE_28_PAIR
A
G
9
A
O6
G
9
1_555
A
U
25
A
N3
U
25
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
A
G
24
A
N1
G
24
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
A
G
24
A
O6
G
24
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
A
G
24
A
N2
G
24
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
A
C
23
A
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
A
C
23
A
N4
C
23
1_555
hydrog
TYPE_28_PAIR
A
U
12
A
N3
U
12
1_555
A
G
22
A
O6
G
22
1_555
hydrog
TYPE_28_PAIR
A
U
12
A
O2
U
12
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
13
A
N3
C
13
1_555
A
G
21
A
N1
G
21
1_555
hydrog
WATSON-CRICK
A
C
13
A
N4
C
13
1_555
A
G
21
A
O6
G
21
1_555
hydrog
WATSON-CRICK
A
C
13
A
O2
C
13
1_555
A
G
21
A
N2
G
21
1_555
hydrog
U-G MISPAIR
A
U
14
A
O2
U
14
1_555
A
G
21
A
N1
G
21
1_555
hydrog
A-G MISPAIR
A
A
27
A
N1
A
27
1_555
A
G
28
A
N2
G
28
1_555
hydrog
G-U MISPAIR
A
G
28
A
N2
G
28
1_555
A
U
29
A
O4
U
29
1_555
RNA
RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, LOOP E MOTIF, HAIRPIN LOOP, RNA
1P5N
PDB
1
1P5N
1
34
1P5N
1
34
1P5N
A
1
1
34