1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kaluarachchi, K.
Rijnbrand, R.
Lemon, S.M.
Gorenstein, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
343
805
817
10.1016/j.jmb.2004.08.095
15476802
Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites
2004
10.2210/pdb1idv/pdb
pdb_00001idv
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
3207.965
HEPATITIS C IRES RNA DOMAIN IIIC
1
syn
polymer
no
no
GGGCGUGCCC
GGGCGUGCCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
-10.843
1
19
A
1
A
10
-12.217
A_G1:C10_A
1
5.838
-0.887
0.145
-0.499
-1.545
1
19
A
2
A
9
0.265
A_G2:C9_A
2
-7.912
0.638
0.096
0.105
0.484
1
19
A
3
A
8
-11.609
A_G3:C8_A
3
-13.270
1.421
1.541
-1.020
3.273
28.256
A
A
1
2
2.631
A
A
10
9
3.340
1.282
0.300
-1.736
AA_G1G2:C9C10_AA
1
2.657
-5.453
28.105
-3.857
0.011
3.939
39.132
A
A
2
3
-5.853
A
A
9
8
3.648
-3.882
-1.577
-0.528
AA_G2G3:C8C9_AA
2
-8.938
13.476
37.946
-0.239
1.090
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2001-10-05
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2001-04-05
REL
Synthesized by in vitro transcription using T7 RNA polymerase
sample
This structure was determined using standard 2D homonuclear techniques.
back calculated data agree with experimental NOESY spectrum
20
10
2D NOESY
2D NOESY
DQF-COSY
2D TOCSY
31P Hetero-TOCSY
1H-13C HSQC
10 mM KCl
6.8
ambient
283
K
10 mM KCl
6.8
ambient
298
K
The structures are based on 254 NOE restraints, 12 sugar pucker restraints and 9 hydrogen bonds
simulated annealing
molecular dynamics
relaxation matrix analysis
10
fewest noe violations
10 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.8
90% H2O/10% D2O
10 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.8
99.996% D2O
BRUNGER
refinement
X-PLOR
3.1
POST, MEADOWS, LUXON and GORENSTEIN
refinement
MORASS
2.51
750
Varian
UNITYPLUS
600
Varian
UNITYPLUS
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
C
4
n
4
C
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
C
9
n
9
C
9
A
C
10
n
10
C
10
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
O2'
H5'
G
U
5
6
1.32
1
A
A
O2'
H5'
G
G
2
3
1.48
1
A
A
O6
H41
G
C
1
10
1.57
2
A
A
O2'
H5'
G
U
5
6
1.55
2
A
A
O2'
H5'
G
G
2
3
1.57
3
A
A
O2'
H5'
G
U
5
6
1.43
4
A
A
O2'
H5'
G
U
5
6
1.13
5
A
A
O2'
H8
C
G
4
5
1.55
6
A
A
O2'
H5'
G
U
5
6
1.30
6
A
A
O6
H41
G
C
1
10
1.53
7
A
A
O2'
H5'
G
G
2
3
1.47
7
A
A
O6
H41
G
C
1
10
1.52
8
A
A
O2'
H5'
G
U
5
6
1.17
8
A
A
O2'
H5'
G
G
2
3
1.40
8
A
A
O6
H41
G
C
2
9
1.57
9
A
A
O2'
H8
C
G
4
5
1.27
9
A
A
O2'
C8
C
G
4
5
1.65
9
A
A
O2'
N7
C
G
4
5
1.74
1
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
1
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
1
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
1
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
1
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
1
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
2
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
2
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
2
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
2
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
2
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
2
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
2
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
2
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
2
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
2
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
3
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
3
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
3
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
3
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
3
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
3
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
3
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
3
-2.75
0.40
106.40
103.65
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
3
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
3
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
4
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
4
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
4
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
4
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
4
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
4
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
4
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
4
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
4
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
4
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
5
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
5
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
5
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
5
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
5
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
5
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
5
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
5
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
5
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
5
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
6
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
6
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
6
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
6
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
6
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
6
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
6
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
6
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
6
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
6
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
7
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
7
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
7
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
7
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
7
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
7
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
7
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
7
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
7
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
7
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
8
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
8
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
8
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
8
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
8
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
8
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
8
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
8
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
8
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
8
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
9
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
9
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
9
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
9
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
9
4.65
0.50
113.10
117.75
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
9
-2.78
0.40
106.40
103.62
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
9
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
9
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
9
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
9
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
10
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
10
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
10
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
10
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
10
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
10
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
10
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
5
5
5
N
10
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
5
5
5
N
10
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
10
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
NMR structure of HCV ires RNA domain IIIC
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
10
A
N3
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
10
A
O2
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
10
A
N4
C
10
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
9
A
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
9
A
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
9
A
N4
C
9
1_555
hydrog
TYPE_7_PAIR
A
G
3
A
N1
G
3
1_555
A
G
7
A
N7
G
7
1_555
hydrog
TYPE_7_PAIR
A
G
3
A
N2
G
3
1_555
A
G
7
A
O6
G
7
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
8
A
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
8
A
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
8
A
N4
C
8
1_555
RNA
Hepatitis C RNA, IRES, Stem-loop, Domain IIIC, RNA
1IDV
PDB
1
1IDV
1
10
1IDV
1
10
1IDV
A
1
1
10