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
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/pdb1f85/pdb
pdb_00001f85
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
4518.731
HCV-1B IRES RNA DOMAIN IIIE
HCV IRES RNA DOMAIN IIIE (NUCLEOTIDES 290-303 OF GENOMIC HEPATITIS C VIRAL RNA)
U290G, G303C
1
syn
polymer
no
no
GGCCUGAUAGGGUC
GGCCUGAUAGGGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-15.101
1
19
A
1
A
14
1.712
A_G1:C14_A
1
-6.686
0.367
-1.036
-0.074
10.193
28
A
2
A
13
-11.080
A_G2:U13_A
2
2.183
-1.715
-0.706
-0.528
33.804
1
19
A
3
A
12
-1.786
A_C3:G12_A
3
-4.435
-0.380
-1.628
-0.194
20.116
1
19
A
4
A
11
0.655
A_C4:G11_A
4
-11.466
-0.261
-1.636
-0.372
-3.815
1
A
5
A
10
33.947
A_U5:G10_A
5
17.838
2.256
-1.210
1.130
-0.275
9
11
A
6
A
9
7.717
A_G6:A9_A
6
1.965
6.732
0.632
-3.314
1.813
17.335
A
A
1
2
26.586
A
A
14
13
2.581
7.553
-0.282
-0.985
AA_G1G2:U13C14_AA
1
-6.139
21.608
14.362
-6.723
-1.873
2.967
40.913
A
A
2
3
-6.167
A
A
13
12
2.806
-4.299
0.884
-1.130
AA_G2C3:G12U13_AA
2
3.389
-4.862
40.561
-1.199
-0.935
2.898
47.236
A
A
3
4
26.667
A
A
12
11
3.594
20.695
0.706
-0.981
AA_C3C4:G11G12_AA
3
3.800
-4.896
42.533
-3.001
-0.555
2.647
29.344
A
A
4
5
27.032
A
A
11
10
4.030
13.213
0.788
-2.068
AA_C4U5:G10G11_AA
4
-1.699
3.476
26.205
-7.159
-1.952
2.449
51.374
A
A
5
6
28.233
A
A
10
9
2.899
23.628
-0.378
-0.259
AA_U5G6:A9G10_AA
5
5.010
-5.986
45.686
-1.714
0.737
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
2000-11-17
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
2000-06-28
REL
REL
Synthesized enzymatically in-vitro using T7 RNA Polymerase
sample
THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. NATURAL ABUNDANCE 13C HMQC EXPERIMENTS WERE PERFORMED.
structures with the least restraint violations,structures with the lowest energy
100
20
31P-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY
10mM
6.40
ambient
283
K
SEE REFERENCE ABOVE
Simulated annealing and restrained molecular dynamics
19
closest to the average
2.5mM RNA, non-isotopically labelled
sodium phosphate buffer, 96% H2O/4% D2O or 100% D2O
BRUNGER
refinement
X-PLOR
3.1
GODDARD
data analysis
Sparky
3.8
VARIAN
processing
VNMR
6.1B
VARIAN
collection
VNMR
6.1B
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
CYT
4
n
4
C
4
A
URA
5
n
5
U
5
A
GUA
6
n
6
G
6
A
ADE
7
n
7
A
7
A
URA
8
n
8
U
8
A
ADE
9
n
9
A
9
A
GUA
10
n
10
G
10
A
GUA
11
n
11
G
11
A
GUA
12
n
12
G
12
A
URA
13
n
13
U
13
A
CYT
14
n
14
C
14
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
2
A
A
O2'
H6
A
U
7
8
1.53
3
A
A
O2'
H6
A
U
7
8
1.53
4
A
A
O2'
H6
A
U
7
8
1.57
5
A
A
O2'
H6
A
U
7
8
1.51
11
A
A
O2'
H6
A
U
7
8
1.50
12
A
A
O2'
H6
A
U
7
8
1.55
13
A
A
O2'
H6
A
U
7
8
1.53
14
A
A
O2'
H6
A
U
7
8
1.56
17
A
A
O2'
H6
A
U
7
8
1.53
18
A
A
O2'
H6
A
U
7
8
1.54
20
A
A
O2'
H5'
G
A
6
7
1.59
SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIIE
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
14
A
N4
C
14
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
N1
G
2
1_555
A
U
13
A
O2
U
13
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
O6
G
2
1_555
A
U
13
A
N3
U
13
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
14
A
N4
C
14
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
12
A
N1
G
12
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
12
A
O6
G
12
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
12
A
N2
G
12
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
11
A
N1
G
11
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
11
A
O6
G
11
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
11
A
N2
G
11
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
12
A
N1
G
12
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
12
A
O6
G
12
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
12
A
N2
G
12
1_555
hydrog
U-G MISPAIR
A
U
5
A
O2
U
5
1_555
A
G
10
A
N1
G
10
1_555
hydrog
TYPE_11_PAIR
A
G
6
A
N2
G
6
1_555
A
A
9
A
N7
A
9
1_555
hydrog
TYPE_11_PAIR
A
G
6
A
N3
G
6
1_555
A
A
9
A
N6
A
9
1_555
hydrog
G-G MISPAIR
A
G
6
A
N2
G
6
1_555
A
G
10
A
O6
G
10
1_555
RNA
Ribonucleic Acid, Hepatitis C virus internal ribosome entry site, Hairpin loop, Tetraloop, RNA structure, RNA
1F85
PDB
1
1F85
1
14
1F85
1
14
1F85
A
1
1
14
1
P 1