1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lescrinier, E.M.
Tessari, M.
van Kuppeveld, F.J.
Melchers, W.J.
Hilbers, C.W.
Heus, H.A.
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
331
759
769
10.1016/S0022-2836(03)00787-3
12909008
Structure of the Pyrimidine-rich Internal Loop in the Poliovirus 3'-UTR: The Importance of Maintaining Pseudo-2-fold Symmetry in RNA Helices Containing Two Adjacent Non-canonical Base-pairs.
2003
10.2210/pdb1n66/pdb
pdb_00001n66
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
7034.227
internal loop in the Y-domain of poliovirus 3'UTR
1
syn
polymer
no
no
GGACCUCUCGAAAGAGUUGUCC
GGACCUCUCGAAAGAGUUGUCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-9.344
1
19
A
1
A
22
-1.242
A_G1:C22_A
1
-9.935
-0.534
0.009
-0.544
7.895
1
19
A
2
A
21
0.319
A_G2:C21_A
2
-14.217
-0.569
-0.019
-0.587
31.810
1
20
A
3
A
20
-1.764
A_A3:U20_A
3
2.590
-0.102
0.307
-0.095
5.421
1
19
A
4
A
19
0.050
A_C4:G19_A
4
3.687
0.297
-1.112
-0.503
-13.858
A
5
A
18
35.199
A_C5:U18_A
5
18.443
2.534
-0.648
-1.450
-32.016
1
16
A
6
A
17
28.306
A_U6:U17_A
6
-16.736
-2.896
0.208
-1.802
-0.921
1
19
A
7
A
16
14.946
A_C7:G16_A
7
-12.511
1.059
-0.607
-0.324
-0.888
1
20
A
8
A
15
-1.168
A_U8:A15_A
8
8.651
0.525
-0.065
-0.346
13.576
1
19
A
9
A
14
4.461
A_C9:G14_A
9
-14.249
0.197
-1.386
-0.559
1.691
10
A
10
A
13
-14.867
A_G10:A13_A
10
-1.138
6.566
0.087
-5.455
2.764
38.096
A
A
1
2
4.676
A
A
22
21
2.771
3.043
-0.935
-1.082
AA_G1G2:C21C22_AA
1
-4.275
6.569
37.746
-1.985
0.972
2.637
37.930
A
A
2
3
1.433
A
A
21
20
2.684
0.931
0.340
-1.172
AA_G2A3:U20C21_AA
2
-1.825
2.809
37.877
-1.899
-0.713
2.772
30.521
A
A
3
4
24.808
A
A
20
19
3.801
12.443
1.108
-2.114
AA_A3C4:G19U20_AA
3
9.902
-19.742
26.135
-6.706
0.036
3.063
36.194
A
A
4
5
16.332
A
A
19
18
4.522
9.828
1.774
-1.694
AA_C4C5:U18G19_AA
4
-12.308
20.453
32.691
-4.418
-4.974
-0.424
26.146
A
A
5
6
53.292
A
A
18
17
3.109
20.895
-0.517
-2.918
AA_C5U6:U17U18_AA
5
-0.150
0.383
15.804
-9.382
1.121
2.066
47.020
A
A
6
7
13.585
A
A
17
16
2.217
10.707
-0.509
0.046
AA_U6C7:G16U17_AA
6
7.852
-9.963
45.208
-0.532
1.070
2.008
33.105
A
A
7
8
34.719
A
A
16
15
3.083
18.661
-1.569
-1.184
AA_C7U8:A15G16_AA
7
-2.198
4.089
27.379
-4.776
2.436
2.870
35.725
A
A
8
9
16.521
A
A
15
14
2.775
9.748
1.604
-0.745
AA_U8C9:G14A15_AA
8
13.959
-23.658
31.524
-2.511
-0.756
3.849
54.540
A
A
9
10
22.796
A
A
14
13
4.069
20.436
-2.060
-0.258
AA_C9G10:A13G14_AA
9
-3.870
4.317
50.702
-1.844
1.952
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
2003-08-19
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
CRYSTAL STRUCTURE OF AN RNA DOUBLE HELIX
INCORPORATING A TRACK OF NON-WATSON-CRICK
BASE PAIRS
NMR structure with GAAA tetraloop
RCSB
Y
RCSB
2002-11-08
REL
REL
structures with the lowest energy
100
20
5.8
ambient
288
K
5.5
ambient
288
K
5.5
ambient
273
K
5.5
ambient
288
K
torsion angle dynamics followed by
conjugate gradient minimization
1
lowest energy
3mM RNA
D2O
3mM RNA
D2O
3mM RNA
90% H2O/10% D2O
1-2mM RNA, U-13C,15N, C-13C,15N
D2O
Varian
collection
VNMR
6.1
Delaglio
processing
NMRPipe
2.1
ETH-Zurich
data analysis
XEASY
1.2.0
Brunger
refinement
X-PLOR
3.851
750
Varian
INOVA
600
Varian
INOVA
500
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
C
4
n
4
C
4
A
C
5
n
5
C
5
A
U
6
n
6
U
6
A
C
7
n
7
C
7
A
U
8
n
8
U
8
A
C
9
n
9
C
9
A
G
10
n
10
G
10
A
A
11
n
11
A
11
A
A
12
n
12
A
12
A
A
13
n
13
A
13
A
G
14
n
14
G
14
A
A
15
n
15
A
15
A
G
16
n
16
G
16
A
U
17
n
17
U
17
A
U
18
n
18
U
18
A
G
19
n
19
G
19
A
U
20
n
20
U
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
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
H3
O2
U
U
6
17
1.36
1
A
A
H21
O2
G
C
1
22
1.51
1
A
A
O2
H3
C
U
5
18
1.52
1
A
A
H21
OP2
G
A
10
13
1.55
1
A
A
H22
N7
G
A
10
13
1.57
2
A
A
H21
OP2
G
A
10
13
1.39
2
A
A
H22
N7
G
A
10
13
1.43
2
A
A
H3
O2
U
U
6
17
1.48
2
A
A
O4
H3
U
U
6
17
1.50
2
A
A
H21
O2
G
C
1
22
1.51
2
A
A
O2
H21
C
G
4
19
1.55
3
A
A
H3
O2
U
U
6
17
1.41
3
A
A
O2
H3
C
U
5
18
1.48
3
A
A
H21
OP2
G
A
10
13
1.48
3
A
A
HO2'
O4'
U
G
18
19
1.51
3
A
A
H21
O2
G
C
1
22
1.51
3
A
A
H1
N3
G
C
2
21
1.57
3
A
A
H22
N7
G
A
10
13
1.57
3
A
A
O2
H21
C
G
4
19
1.58
4
A
A
O4
H3
U
U
6
17
1.48
4
A
A
H21
OP2
G
A
10
13
1.50
4
A
A
H22
N7
G
A
10
13
1.54
4
A
A
H21
O2
G
C
1
22
1.56
4
A
A
O6
H41
G
C
1
22
1.57
4
A
A
O2
H21
C
G
7
16
1.59
5
A
A
H21
O2
G
C
1
22
1.48
5
A
A
O2
H3
C
U
5
18
1.48
5
A
A
H3
O2
U
U
6
17
1.49
5
A
A
H21
OP2
G
A
10
13
1.50
5
A
A
O2
H21
C
G
4
19
1.56
5
A
A
O6
H41
G
C
2
21
1.58
5
A
A
H1
N3
G
C
2
21
1.58
5
A
A
H22
N7
G
A
10
13
1.58
6
A
A
H3
O2
U
U
6
17
1.48
6
A
A
H21
O2
G
C
1
22
1.49
6
A
A
O2
H3
C
U
5
18
1.51
6
A
A
H1
N3
G
C
2
21
1.53
6
A
A
O6
H41
G
C
2
21
1.54
6
A
A
O4
H3
U
U
6
17
1.56
6
A
A
H21
O2
G
C
2
21
1.59
6
A
A
O2
H21
C
G
4
19
1.60
6
A
A
H21
OP2
G
A
10
13
1.60
7
A
A
H22
N7
G
A
10
13
1.44
7
A
A
H21
O2
G
C
1
22
1.47
7
A
A
H21
OP2
G
A
10
13
1.48
7
A
A
O4
H3
U
U
6
17
1.48
7
A
A
O2
H3
C
U
5
18
1.56
7
A
A
O6
H41
G
C
2
21
1.57
7
A
A
H1
N3
G
C
2
21
1.59
8
A
A
O2
H3
C
U
5
18
1.41
8
A
A
H3
O2
U
U
6
17
1.42
8
A
A
H21
O2
G
C
1
22
1.49
8
A
A
O2
H21
C
G
4
19
1.56
8
A
A
H1
N3
G
C
2
21
1.57
9
A
A
H3
O2
U
U
6
17
1.43
9
A
A
O2
H3
C
U
5
18
1.47
9
A
A
H21
O2
G
C
1
22
1.55
9
A
A
H22
N7
G
A
10
13
1.56
9
A
A
H21
OP2
G
A
10
13
1.57
9
A
A
O2
H21
C
G
4
19
1.57
10
A
A
HO2'
OP1
G
A
10
11
1.48
10
A
A
H22
N7
G
A
10
13
1.49
10
A
A
H3
O2
U
U
6
17
1.53
10
A
A
H21
O2
G
C
1
22
1.53
10
A
A
O2
H21
C
G
4
19
1.55
10
A
A
O2
H3
C
U
5
18
1.57
10
A
A
H1
N3
G
C
2
21
1.59
11
A
A
H3
O2
U
U
6
17
1.41
11
A
A
O2
H3
C
U
5
18
1.47
11
A
A
H21
O2
G
C
1
22
1.52
12
A
A
H21
OP2
G
A
10
13
1.38
12
A
A
H22
N7
G
A
10
13
1.43
12
A
A
H21
O2
G
C
1
22
1.47
12
A
A
H1
N3
G
C
2
21
1.53
12
A
A
O2
H21
C
G
4
19
1.54
12
A
A
O4
H3
U
U
6
17
1.55
12
A
A
O6
H41
G
C
2
21
1.56
12
A
A
O2
H3
C
U
5
18
1.56
12
A
A
H1
N3
G
C
1
22
1.60
13
A
A
O4
H3
U
U
6
17
1.42
13
A
A
H21
O2
G
C
1
22
1.51
13
A
A
H41
O6
C
G
9
14
1.59
13
A
A
O2
H21
C
G
4
19
1.60
14
A
A
H3
O2
U
U
6
17
1.42
14
A
A
H1
N3
G
C
2
21
1.53
14
A
A
O2
H3
C
U
5
18
1.53
14
A
A
H21
O2
G
C
1
22
1.53
14
A
A
O6
H41
G
C
2
21
1.54
14
A
A
H21
OP2
G
A
10
13
1.57
14
A
A
H22
N7
G
A
10
13
1.59
14
A
A
O6
H41
G
C
1
22
1.59
14
A
A
O2
H21
C
G
4
19
1.60
15
A
A
O4
H3
U
U
6
17
1.46
15
A
A
H21
O2
G
C
1
22
1.50
15
A
A
H21
OP2
G
A
10
13
1.51
15
A
A
H3
O2
U
U
6
17
1.51
15
A
A
O2
H3
C
U
5
18
1.55
15
A
A
H22
N7
G
A
10
13
1.59
15
A
A
O2
H21
C
G
7
16
1.59
16
A
A
O2
H3
C
U
5
18
1.36
16
A
A
H3
O2
U
U
6
17
1.40
16
A
A
O2
H21
C
G
4
19
1.52
16
A
A
H21
O2
G
C
1
22
1.58
17
A
A
O4
H3
U
U
6
17
1.48
17
A
A
H3
O2
U
U
6
17
1.48
17
A
A
H21
OP2
G
A
10
13
1.49
17
A
A
H22
N7
G
A
10
13
1.56
18
A
A
HO2'
OP1
G
G
1
2
1.39
18
A
A
H21
OP2
G
A
10
13
1.45
18
A
A
H3
O2
U
U
6
17
1.49
18
A
A
O6
H41
G
C
2
21
1.49
18
A
A
O2
H3
C
U
5
18
1.51
18
A
A
H21
O2
G
C
2
21
1.56
18
A
A
H22
N7
G
A
10
13
1.58
18
A
A
O2
H21
C
G
4
19
1.58
19
A
A
H21
O2
G
C
1
22
1.46
19
A
A
H3
O2
U
U
6
17
1.56
19
A
A
H21
OP2
G
A
10
13
1.56
19
A
A
O2
H21
C
G
4
19
1.59
20
A
A
O2
H21
C
G
4
19
1.49
20
A
A
H3
O2
U
U
6
17
1.52
20
A
A
H22
N7
G
A
10
13
1.53
20
A
A
H21
O2
G
C
1
22
1.54
Structure of the pyrimidine-rich internal loop in the Y-domain of poliovirus 3'UTR
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
22
A
N4
C
22
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
21
A
N4
C
21
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
U
20
A
N3
U
20
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
20
A
O4
U
20
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
19
A
N2
G
19
1_555
hydrog
C-U MISPAIR
A
C
5
A
O2
C
5
1_555
A
U
18
A
N3
U
18
1_555
hydrog
TYPE_16_PAIR
A
U
6
A
N3
U
6
1_555
A
U
17
A
O2
U
17
1_555
hydrog
TYPE_16_PAIR
A
U
6
A
O4
U
6
1_555
A
U
17
A
N3
U
17
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
A
A
15
A
N1
A
15
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
A
A
15
A
N6
A
15
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
A
G
14
A
N1
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
A
G
14
A
O6
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
A
G
14
A
N2
G
14
1_555
hydrog
C-A MISPAIR
A
C
9
A
N3
C
9
1_555
A
A
15
A
N6
A
15
1_555
hydrog
G-A MISPAIR
A
G
10
A
N2
G
10
1_555
A
A
13
A
N7
A
13
1_555
RNA
RNA internal loop, RNA
1N66
PDB
1
1N66
1
22
1N66
1
22
1N66
A
1
1
22
1
P 1