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/pdb1p5m/pdb
pdb_00001p5m
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
17625.432
55-MER
HCV IRES domain IIa (residues 45-69,98-117)
1
syn
polymer
no
no
GGCUGUGAGGAACUACUGUCUUCACGCCUUCGGGAGUGUCGUGCAGCCUCCAGCC
GGCUGUGAGGAACUACUGUCUUCACGCCUUCGGGAGUGUCGUGCAGCCUCCAGCC
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
43.754
1
A
1
A
55
-2.445
A_G1:C55_A
1
-42.911
-0.501
0.385
-0.148
18.600
A
2
A
54
-16.352
A_G2:C54_A
2
-34.850
0.502
0.326
-0.138
10.685
1
19
A
3
A
53
1.887
A_C3:G53_A
3
-30.524
-0.579
0.569
-0.108
15.715
1
20
A
4
A
52
-6.044
A_U4:A52_A
4
-11.740
-0.745
0.552
-0.122
-6.240
1
19
A
5
A
51
4.877
A_G5:C51_A
5
-25.631
0.380
0.301
-0.035
-17.598
1
19
A
7
A
50
5.249
A_G7:C50_A
6
-25.779
0.378
-0.133
-0.005
-20.611
1
20
A
8
A
49
11.316
A_A8:U49_A
7
-23.087
-0.215
0.189
-0.107
-12.579
1
19
A
9
A
48
4.560
A_G9:C48_A
8
-23.360
0.553
0.100
-0.038
10.763
1
19
A
10
A
47
-6.989
A_G10:C47_A
9
-9.433
0.464
0.597
-0.148
7.901
1
19
A
16
A
46
4.727
A_C16:G46_A
10
-27.520
-0.302
0.011
-0.083
10.318
1
20
A
17
A
45
5.084
A_U17:A45_A
11
-17.800
0.708
0.546
-0.354
5.878
1
19
A
18
A
44
-6.006
A_G18:C44_A
12
-29.082
0.214
-0.294
-0.273
-4.471
28
A
19
A
43
-9.289
A_U19:G43_A
13
-16.719
2.196
-0.338
-0.598
2.550
1
19
A
20
A
41
-5.579
A_C20:G41_A
14
2.174
-0.410
-0.306
-0.140
18.598
1
18
A
21
A
40
18.879
A_U21:C40_A
15
-12.085
-0.226
-0.208
-1.592
-1.887
A
22
A
39
4.149
A_U22:U39_A
16
-29.552
-1.066
-1.178
-1.564
5.020
1
19
A
23
A
38
2.765
A_C23:G38_A
17
-17.741
-0.577
-1.337
-0.457
0.063
1
20
A
24
A
37
-0.455
A_A24:U37_A
18
-10.244
-0.325
-0.621
-0.421
21.486
1
19
A
25
A
36
-0.960
A_C25:G36_A
19
-14.962
-0.202
-0.926
-0.167
7.012
A
26
A
35
76.815
A_G26:A35_A
20
-11.140
0.244
1.955
-3.956
2.628
1
19
A
27
A
34
-0.344
A_C27:G34_A
21
7.566
-0.371
0.152
-0.089
26.500
1
19
A
28
A
33
-7.180
A_C28:G33_A
22
-6.335
-0.361
-1.668
-0.347
-2.444
A
29
A
32
-79.769
A_U29:G32_A
23
-21.814
2.276
-0.084
-4.053
3.589
39.864
A
A
1
2
23.778
A
A
55
54
4.044
15.795
-0.721
-0.459
AA_G1G2:C54C55_AA
1
-1.887
2.841
36.671
-2.900
0.791
3.256
37.954
A
A
2
3
-8.926
A
A
54
53
2.960
-5.777
1.789
-1.244
AA_G2C3:G53C54_AA
2
3.449
-5.329
37.375
-1.206
-2.329
3.415
29.953
A
A
3
4
-14.093
A
A
53
52
3.231
-7.197
0.137
-1.348
AA_C3U4:A52G53_AA
3
-3.781
7.404
28.853
-1.068
-1.074
3.475
34.671
A
A
4
5
4.520
A
A
52
51
3.604
2.688
0.345
-1.787
AA_U4G5:C51A52_AA
4
2.726
-4.583
34.465
-3.446
-0.125
2.908
37.379
A
A
5
7
14.490
A
A
51
50
3.231
9.196
-0.807
-0.879
AA_G5G7:C50C51_AA
5
0.953
-1.502
36.257
-2.526
1.380
2.628
39.013
A
A
7
8
12.869
A
A
50
49
2.896
8.528
0.190
-0.923
AA_G7A8:U49C50_AA
6
-1.586
2.393
38.073
-2.262
-0.448
2.560
33.639
A
A
8
9
16.396
A
A
49
48
2.844
9.370
-0.693
-0.677
AA_A8G9:C48U49_AA
7
-0.322
0.563
32.342
-2.460
1.153
2.338
33.822
A
A
9
10
5.084
A
A
48
47
2.417
2.948
-0.064
-0.734
AA_G9G10:C47C48_AA
8
-3.943
6.801
33.473
-1.610
-0.356
2.816
40.399
A
A
16
17
24.108
A
A
46
45
3.169
16.183
-0.237
-0.289
AA_C16U17:A45G46_AA
9
-4.426
6.593
36.883
-2.167
-0.135
2.105
37.620
A
A
17
18
28.043
A
A
45
44
3.043
17.328
-0.693
-0.959
AA_U17G18:C44A45_AA
10
7.133
-11.543
32.768
-3.395
1.860
3.361
51.166
A
A
18
19
-3.375
A
A
44
43
3.289
-2.913
0.805
-0.795
AA_G18U19:G43C44_AA
11
2.630
-3.048
51.025
-0.716
-0.747
2.992
26.809
A
A
19
20
4.078
A
A
43
41
3.158
1.888
0.510
-1.679
AA_U19C20:G41G43_AA
12
-1.859
4.016
26.680
-4.080
-1.552
2.645
36.245
A
A
20
21
35.126
A
A
41
40
2.992
20.597
1.210
0.465
AA_C20U21:C40G41_AA
13
-2.785
4.750
29.859
-2.005
-2.317
3.957
38.763
A
A
21
22
8.855
A
A
40
39
4.374
5.801
-0.613
-0.712
AA_U21U22:U39C40_AA
14
9.462
-14.443
37.199
-1.997
2.430
2.761
36.178
A
A
22
23
12.426
A
A
39
38
2.898
7.659
-0.707
-0.497
AA_U22C23:G38U39_AA
15
-1.495
2.425
35.354
-1.745
0.955
3.022
34.164
A
A
23
24
39.854
A
A
38
37
3.657
21.579
-0.103
0.325
AA_C23A24:U37G38_AA
16
-5.757
10.632
26.020
-3.441
-0.891
2.705
37.096
A
A
24
25
-0.418
A
A
37
36
2.663
-0.266
0.692
-0.941
AA_A24C25:G36U37_AA
17
2.172
-3.416
37.034
-1.450
-0.849
-0.504
-179.947
A
A
25
26
8.100
A
A
36
35
-0.509
-16.200
-0.651
4.469
AA_C25G26:A35G36_AA
18
166.887
83.443
-179.505
-2.234
-0.327
0.979
-170.536
A
A
26
27
47.224
A
A
35
34
-3.168
-90.111
-3.455
-2.814
AA_G26C27:G34A35_AA
19
144.670
75.816
-16.316
0.909
-2.541
2.536
30.048
A
A
27
28
2.351
A
A
34
33
2.736
1.194
0.032
-1.105
AA_C27C28:G33G34_AA
20
10.509
-20.694
28.165
-2.335
1.735
3.463
101.804
A
A
28
29
8.090
A
A
33
32
3.623
12.540
1.860
-1.912
AA_C28U29:G32G33_AA
21
1.935
-1.248
101.229
-1.436
-1.167
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
22
2D S-NOESY
2D NOESY
DQF-COSY
2D HP-COSY
3D_13C-separated_NOESY
3D HCP
3D HMQC TOCSY
100mM NaCl, 5mM MgCl2
6.40
ambient
288
K
100mM NaCl, 5mM MgCl2
6.40
ambient
298
K
100mM NaCl, 5mM MgCl2
6.40
ambient
303
K
see reference above
see reference above
1
closest to the average
1-2mM HCV IRES domain IIa RNA
10mM phosphate buffer
100mM sodium chloride
5mM magnesium chloride
96% D2O, 4% H2O
1-2mM HCV IRES domain IIa RNA
10mM phosphate buffer
100mM sodium chloride
5mM magnesium chloride
100% D2O
1mM HCV IRES domain IIa RNA
U-15N,13C
10mM phosphate buffer
100mM sodium chloride
5mM magnesium chloride
96% D2O, 4% H2O
1mM HCV IRES domain IIa RNA
U-15N,13C
10mM phosphate buffer
100mM sodium chloride
5mM magnesium chloride
100% D2O
Varian
processing
VNMR
6.1C
Goddard, Kneller
data analysis
Sparky
3
Brunger
refinement
X-PLOR
3.1
Brunger
refinement
CNS
1.1
Zweckstetter, Bax
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
URI
4
n
4
U
4
A
GUA
5
n
5
G
5
A
URI
6
n
6
U
6
A
GUA
7
n
7
G
7
A
ADE
8
n
8
A
8
A
GUA
9
n
9
G
9
A
GUA
10
n
10
G
10
A
ADE
11
n
11
A
11
A
ADE
12
n
12
A
12
A
CYT
13
n
13
C
13
A
URI
14
n
14
U
14
A
ADE
15
n
15
A
15
A
CYT
16
n
16
C
16
A
URI
17
n
17
U
17
A
GUA
18
n
18
G
18
A
URI
19
n
19
U
19
A
CYT
20
n
20
C
20
A
URI
21
n
21
U
21
A
URI
22
n
22
U
22
A
CYT
23
n
23
C
23
A
ADE
24
n
24
A
24
A
CYT
25
n
25
C
25
A
GUA
26
n
26
G
26
A
CYT
27
n
27
C
27
A
CYT
28
n
28
C
28
A
URI
29
n
29
U
29
A
URI
30
n
30
U
30
A
CYT
31
n
31
C
31
A
GUA
32
n
32
G
32
A
GUA
33
n
33
G
33
A
GUA
34
n
34
G
34
A
ADE
35
n
35
A
35
A
GUA
36
n
36
G
36
A
URI
37
n
37
U
37
A
GUA
38
n
38
G
38
A
URI
39
n
39
U
39
A
CYT
40
n
40
C
40
A
GUA
41
n
41
G
41
A
URI
42
n
42
U
42
A
GUA
43
n
43
G
43
A
CYT
44
n
44
C
44
A
ADE
45
n
45
A
45
A
GUA
46
n
46
G
46
A
CYT
47
n
47
C
47
A
CYT
48
n
48
C
48
A
URI
49
n
49
U
49
A
CYT
50
n
50
C
50
A
CYT
51
n
51
C
51
A
ADE
52
n
52
A
52
A
GUA
53
n
53
G
53
A
CYT
54
n
54
C
54
A
CYT
55
n
55
C
55
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
18
A
A
O6
H41
G
C
18
44
1.60
19
A
A
HO2'
O4'
G
C
26
27
1.57
21
A
A
O6
H41
G
C
18
44
1.59
Solution Structure of HCV IRES Domain IIa
1
N
N
hydrog
G-C PAIR
A
G
1
A
N1
G
1
1_555
A
C
55
A
O2
C
55
1_555
hydrog
G-G MISPAIR
A
G
2
A
O6
G
2
1_555
A
G
53
A
N1
G
53
1_555
hydrog
G-C PAIR
A
G
2
A
N1
G
2
1_555
A
C
54
A
N3
C
54
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
53
A
N1
G
53
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
53
A
O6
G
53
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
53
A
N2
G
53
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
A
A
52
A
N1
A
52
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
A
A
52
A
N6
A
52
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
51
A
N3
C
51
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
51
A
O2
C
51
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
51
A
N4
C
51
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
A
C
50
A
N3
C
50
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
A
C
50
A
O2
C
50
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
A
C
50
A
N4
C
50
1_555
hydrog
WATSON-CRICK
A
A
8
A
N1
A
8
1_555
A
U
49
A
N3
U
49
1_555
hydrog
WATSON-CRICK
A
A
8
A
N6
A
8
1_555
A
U
49
A
O4
U
49
1_555
hydrog
G-C PAIR
A
G
9
A
O6
G
9
1_555
A
C
47
A
N4
C
47
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
48
A
N3
C
48
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
48
A
O2
C
48
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
48
A
N4
C
48
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
47
A
N3
C
47
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
47
A
O2
C
47
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
47
A
N4
C
47
1_555
hydrog
WATSON-CRICK
A
C
16
A
N3
C
16
1_555
A
G
46
A
N1
G
46
1_555
hydrog
WATSON-CRICK
A
C
16
A
N4
C
16
1_555
A
G
46
A
O6
G
46
1_555
hydrog
WATSON-CRICK
A
C
16
A
O2
C
16
1_555
A
G
46
A
N2
G
46
1_555
hydrog
WATSON-CRICK
A
U
17
A
N3
U
17
1_555
A
A
45
A
N1
A
45
1_555
hydrog
WATSON-CRICK
A
U
17
A
O4
U
17
1_555
A
A
45
A
N6
A
45
1_555
hydrog
WATSON-CRICK
A
G
18
A
N1
G
18
1_555
A
C
44
A
N3
C
44
1_555
hydrog
WATSON-CRICK
A
G
18
A
N2
G
18
1_555
A
C
44
A
O2
C
44
1_555
hydrog
WATSON-CRICK
A
G
18
A
O6
G
18
1_555
A
C
44
A
N4
C
44
1_555
hydrog
TYPE_28_PAIR
A
U
19
A
N3
U
19
1_555
A
G
43
A
O6
G
43
1_555
hydrog
TYPE_28_PAIR
A
U
19
A
O2
U
19
1_555
A
G
43
A
N1
G
43
1_555
hydrog
WATSON-CRICK
A
C
20
A
N3
C
20
1_555
A
G
41
A
N1
G
41
1_555
hydrog
WATSON-CRICK
A
C
20
A
N4
C
20
1_555
A
G
41
A
O6
G
41
1_555
hydrog
WATSON-CRICK
A
C
20
A
O2
C
20
1_555
A
G
41
A
N2
G
41
1_555
hydrog
TYPE_18_PAIR
A
U
21
A
N3
U
21
1_555
A
C
40
A
N3
C
40
1_555
hydrog
TYPE_18_PAIR
A
U
21
A
O4
U
21
1_555
A
C
40
A
N4
C
40
1_555
hydrog
U-U MISPAIR
A
U
22
A
O4
U
22
1_555
A
U
39
A
N3
U
39
1_555
hydrog
WATSON-CRICK
A
C
23
A
N3
C
23
1_555
A
G
38
A
N1
G
38
1_555
hydrog
WATSON-CRICK
A
C
23
A
N4
C
23
1_555
A
G
38
A
O6
G
38
1_555
hydrog
WATSON-CRICK
A
C
23
A
O2
C
23
1_555
A
G
38
A
N2
G
38
1_555
hydrog
WATSON-CRICK
A
A
24
A
N1
A
24
1_555
A
U
37
A
N3
U
37
1_555
hydrog
WATSON-CRICK
A
A
24
A
N6
A
24
1_555
A
U
37
A
O4
U
37
1_555
hydrog
WATSON-CRICK
A
C
25
A
N3
C
25
1_555
A
G
36
A
N1
G
36
1_555
hydrog
WATSON-CRICK
A
C
25
A
N4
C
25
1_555
A
G
36
A
O6
G
36
1_555
hydrog
WATSON-CRICK
A
C
25
A
O2
C
25
1_555
A
G
36
A
N2
G
36
1_555
hydrog
G-A MISPAIR
A
G
26
A
O6
G
26
1_555
A
A
35
A
N6
A
35
1_555
hydrog
WATSON-CRICK
A
C
27
A
N3
C
27
1_555
A
G
34
A
N1
G
34
1_555
hydrog
WATSON-CRICK
A
C
27
A
N4
C
27
1_555
A
G
34
A
O6
G
34
1_555
hydrog
WATSON-CRICK
A
C
27
A
O2
C
27
1_555
A
G
34
A
N2
G
34
1_555
hydrog
WATSON-CRICK
A
C
28
A
N3
C
28
1_555
A
G
33
A
N1
G
33
1_555
hydrog
WATSON-CRICK
A
C
28
A
N4
C
28
1_555
A
G
33
A
O6
G
33
1_555
hydrog
WATSON-CRICK
A
C
28
A
O2
C
28
1_555
A
G
33
A
N2
G
33
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
U-G MISPAIR
A
U
29
A
O2
U
29
1_555
A
G
32
A
N1
G
32
1_555
RNA
RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, tRNA, RNA
1P5M
PDB
1
1P5M
1
55
1P5M
1
55
1P5M
A
1
1
55