1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yuan, Y.
Kerwood, D.J.
Paoletti, A.C.
Shubsda, M.F.
Borer, P.N.
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
Biochemistry
BICHAW
0033
0006-2960
42
5259
5269
10.1021/bi034084a
12731867
Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop
2003
10.2210/pdb1osw/pdb
pdb_00001osw
CHIRALITY ERRORS EXIST IN SOME MODELS.
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
stem of SL1 RNA
7472.528
5'-R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP*CP*UP*CP*CP*A)-3'
1
syn
polymer
no
no
GGAGGCGCUACGGCGAGGCUCCA
GGAGGCGCUACGGCGAGGCUCCA
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
-25.698
1
19
A
1
A
22
-1.669
A_G1:C22_A
1
-11.764
-0.347
-0.344
0.051
-19.201
1
19
A
2
A
21
-3.455
A_G2:C21_A
2
-13.755
-0.246
-0.270
0.090
-14.790
1
20
A
3
A
20
-3.702
A_A3:U20_A
3
-15.385
-0.049
-0.176
0.111
-36.587
1
19
A
4
A
19
2.737
A_G4:C19_A
4
-37.646
-0.627
-0.619
0.057
13.144
1
8
A
5
A
16
-20.772
A_G5:A16_A
5
8.071
0.573
-0.307
1.704
12.731
1
19
A
6
A
15
1.248
A_C6:G15_A
6
-15.863
0.281
-0.587
0.038
13.792
1
19
A
7
A
14
2.916
A_G7:C14_A
7
-10.972
-1.000
-0.101
-0.161
23.123
1
19
A
8
A
13
-3.433
A_C8:G13_A
8
-1.379
0.102
-0.265
0.108
-8.775
2
A
9
A
12
-151.640
A_U9:G12_A
9
-47.768
0.148
0.370
-5.336
3.009
29.433
A
A
1
2
8.814
A
A
22
21
3.316
4.422
0.532
-2.066
AA_G1G2:C21C22_AA
1
6.882
-13.719
28.298
-5.000
0.405
3.062
30.342
A
A
2
3
6.857
A
A
21
20
3.278
3.577
0.191
-1.727
AA_G2A3:U20C21_AA
2
2.483
-4.760
30.035
-4.001
0.122
3.504
32.466
A
A
3
4
17.367
A
A
20
19
4.104
9.533
0.158
-1.397
AA_A3G4:C19U20_AA
3
5.138
-9.360
30.652
-4.504
0.797
3.666
78.274
A
A
4
5
-14.189
A
A
19
16
5.084
-16.980
1.958
-2.102
AA_G4G5:A16C19_AA
4
-44.804
37.441
63.847
-0.935
-3.477
2.395
24.768
A
A
5
6
18.214
A
A
16
15
3.255
7.681
0.510
-2.166
AA_G5C6:G15A16_AA
5
-1.697
4.024
23.504
-7.115
-1.644
2.665
40.342
A
A
6
7
31.903
A
A
15
14
3.397
20.958
-0.169
-0.529
AA_C6G7:C14G15_AA
6
-4.298
6.543
34.405
-3.150
-0.244
2.846
30.850
A
A
7
8
17.349
A
A
14
13
3.249
9.097
-0.354
-0.948
AA_G7C8:G13C14_AA
7
-0.907
1.730
29.496
-3.471
0.497
2.484
95.128
A
A
8
9
13.636
A
A
13
12
2.785
20.004
-4.226
1.165
AA_C8U9:G12G13_AA
8
12.786
-8.716
92.817
0.498
3.050
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
2003-05-20
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
2003-03-20
REL
REL
RNA sequence obtained from Dharmacon
sample
Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation.
structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function
50
23
2D NOESY
2D TOCSY
HP-COSY
2D NOESY
H-C HSQC
25 mM NaCl
6.3
ambient
300
K
25 mM NaCl
5.5
ambient
278
K
DYANA followed by molecular dynamics using AMBER
17
closest to the average
1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3
99.996% D2O or 90% D2O, 10% H2O
Bruker
collection
XwinNMR
2.6
Tripos
processing
NMRZ/TRIAD
6.1
University of California, San Francisco
iterative matrix relaxation
MARDIGRAS
3.2
Guntert, P., Mumenthaler, C. and Wuthrich, K.
structure solution
DYANA
1.5
University of California, San Francisco
refinement
Amber
5.0
500
Bruker
DRX
600
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
U
9
n
9
U
9
A
A
10
n
10
A
10
A
C
11
n
11
C
11
A
G
12
n
12
G
12
A
G
13
n
13
G
13
A
C
14
n
14
C
14
A
G
15
n
15
G
15
A
A
16
n
16
A
16
A
G
17
n
17
G
17
A
G
18
n
18
G
18
A
C
19
n
19
C
19
A
U
20
n
20
U
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
A
n
23
23
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
23
A
A
23
1
Y
2
A
A
23
A
A
23
1
Y
3
A
A
23
A
A
23
1
Y
4
A
A
23
A
A
23
1
Y
5
A
A
23
A
A
23
1
Y
6
A
A
23
A
A
23
1
Y
7
A
A
23
A
A
23
1
Y
8
A
A
23
A
A
23
1
Y
9
A
A
23
A
A
23
1
Y
10
A
A
23
A
A
23
1
Y
11
A
A
23
A
A
23
1
Y
12
A
A
23
A
A
23
1
Y
13
A
A
23
A
A
23
1
Y
14
A
A
23
A
A
23
1
Y
15
A
A
23
A
A
23
1
Y
16
A
A
23
A
A
23
1
Y
17
A
A
23
A
A
23
1
Y
18
A
A
23
A
A
23
1
Y
19
A
A
23
A
A
23
1
Y
20
A
A
23
A
A
23
1
Y
21
A
A
23
A
A
23
1
Y
22
A
A
23
A
A
23
1
Y
23
A
A
23
A
A
23
1
Y
1
A
G
12
0.068
SIDE CHAIN
2
A
G
7
0.056
SIDE CHAIN
2
A
C
14
0.069
SIDE CHAIN
3
A
G
4
0.067
SIDE CHAIN
3
A
G
18
0.073
SIDE CHAIN
4
A
U
9
0.072
SIDE CHAIN
4
A
G
18
0.078
SIDE CHAIN
4
A
U
20
0.060
SIDE CHAIN
4
A
C
21
0.065
SIDE CHAIN
5
A
C
6
0.078
SIDE CHAIN
5
A
G
18
0.061
SIDE CHAIN
6
A
G
12
0.055
SIDE CHAIN
6
A
G
13
0.076
SIDE CHAIN
7
A
G
7
0.061
SIDE CHAIN
7
A
U
9
0.065
SIDE CHAIN
7
A
G
12
0.057
SIDE CHAIN
7
A
C
19
0.098
SIDE CHAIN
7
A
U
20
0.072
SIDE CHAIN
8
A
U
9
0.098
SIDE CHAIN
8
A
C
21
0.058
SIDE CHAIN
9
A
U
9
0.076
SIDE CHAIN
9
A
G
18
0.088
SIDE CHAIN
10
A
U
9
0.074
SIDE CHAIN
11
A
G
1
0.061
SIDE CHAIN
11
A
G
18
0.076
SIDE CHAIN
13
A
U
9
0.087
SIDE CHAIN
13
A
G
13
0.080
SIDE CHAIN
13
A
G
18
0.049
SIDE CHAIN
13
A
U
20
0.063
SIDE CHAIN
14
A
G
4
0.055
SIDE CHAIN
14
A
U
9
0.076
SIDE CHAIN
14
A
G
12
0.059
SIDE CHAIN
14
A
G
18
0.052
SIDE CHAIN
15
A
G
7
0.050
SIDE CHAIN
15
A
G
12
0.053
SIDE CHAIN
16
A
C
11
0.085
SIDE CHAIN
17
A
G
7
0.056
SIDE CHAIN
17
A
C
19
0.081
SIDE CHAIN
17
A
C
21
0.078
SIDE CHAIN
18
A
C
11
0.066
SIDE CHAIN
18
A
C
14
0.073
SIDE CHAIN
19
A
G
17
0.060
SIDE CHAIN
19
A
G
18
0.056
SIDE CHAIN
20
A
G
7
0.058
SIDE CHAIN
20
A
C
19
0.087
SIDE CHAIN
21
A
G
7
0.056
SIDE CHAIN
21
A
G
12
0.064
SIDE CHAIN
21
A
A
16
0.063
SIDE CHAIN
22
A
G
5
0.054
SIDE CHAIN
22
A
G
7
0.058
SIDE CHAIN
22
A
U
9
0.087
SIDE CHAIN
22
A
G
12
0.080
SIDE CHAIN
22
A
G
13
0.051
SIDE CHAIN
22
A
G
18
0.067
SIDE CHAIN
22
A
C
22
0.090
SIDE CHAIN
23
A
C
14
0.096
SIDE CHAIN
23
A
G
18
0.055
SIDE CHAIN
1
5.40
0.70
108.50
113.90
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
1
6.09
0.70
108.50
114.59
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
1
8.21
1.20
119.70
127.91
A
A
A
C3'
O3'
P
G
G
C
18
18
19
Y
1
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
2
4.81
0.70
108.50
113.31
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
2
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
3
5.73
0.70
108.50
114.23
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
4
4.48
0.70
108.50
112.98
A
A
A
O4'
C1'
N9
A
A
A
3
3
3
N
4
5.40
0.70
108.50
113.90
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
4
4.45
0.70
108.50
112.95
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
4
4.61
0.70
108.50
113.11
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
5
5.06
0.70
108.50
113.56
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
6
4.72
0.70
108.50
113.22
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
6
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
7
5.00
0.70
108.50
113.50
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
7
-4.31
0.70
109.70
105.39
A
A
A
C1'
O4'
C4'
G
G
G
12
12
12
N
7
5.97
0.70
108.50
114.47
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
7
5.42
0.70
108.50
113.92
A
A
A
O4'
C1'
N1
C
C
C
21
21
21
N
8
5.14
0.70
108.50
113.64
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
8
4.72
0.70
108.50
113.22
A
A
A
O4'
C1'
N1
C
C
C
21
21
21
N
8
4.37
0.70
108.50
112.87
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
9
5.44
0.70
108.50
113.94
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
9
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
C
C
C
19
19
19
N
10
4.82
0.70
108.50
113.32
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
10
4.90
0.70
108.50
113.40
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
10
5.15
0.70
108.50
113.65
A
A
A
O4'
C1'
N9
G
G
G
17
17
17
N
11
4.51
0.70
108.50
113.01
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
11
4.45
0.70
108.50
112.95
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
12
5.09
0.70
108.50
113.59
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
13
5.34
0.70
108.50
113.84
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
13
4.43
0.70
108.50
112.93
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
14
5.14
0.70
108.50
113.64
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
15
4.58
0.70
108.50
113.08
A
A
A
O4'
C1'
N9
G
G
G
18
18
18
N
15
8.35
1.20
119.70
128.05
A
A
A
C3'
O3'
P
G
G
C
18
18
19
Y
16
5.16
0.70
108.50
113.66
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
16
4.37
0.70
108.50
112.87
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
16
5.24
0.70
108.50
113.74
A
A
A
O4'
C1'
N1
C
C
C
19
19
19
N
16
4.43
0.70
108.50
112.93
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
17
4.92
0.70
108.50
113.42
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
17
-3.10
0.50
128.60
125.50
A
A
A
N3
C4
C5
G
G
G
12
12
12
N
18
4.60
0.70
108.50
113.10
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
18
5.68
0.70
108.50
114.18
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
18
4.54
0.70
108.50
113.04
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
19
5.05
0.70
108.50
113.55
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
19
4.68
0.70
108.50
113.18
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
19
4.40
0.70
108.50
112.90
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
20
4.67
0.70
108.50
113.17
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
20
4.77
0.70
108.50
113.27
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
20
4.62
0.70
108.50
113.12
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
20
4.51
0.70
108.50
113.01
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
20
4.44
0.70
108.50
112.94
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
21
5.27
0.70
108.50
113.77
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
21
4.68
0.70
108.50
113.18
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
22
4.32
0.70
108.50
112.82
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
22
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
22
4.73
0.70
108.50
113.23
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
23
5.37
0.70
108.50
113.87
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
23
6.15
0.70
108.50
114.65
A
A
A
O4'
C1'
N1
C
C
C
14
14
14
N
23
4.62
0.70
108.50
113.12
A
A
A
O4'
C1'
N1
U
U
U
20
20
20
N
23
4.44
0.70
108.50
112.94
A
A
A
O4'
C1'
N1
C
C
C
21
21
21
N
23
4.22
0.70
108.50
112.72
A
A
A
O4'
C1'
N1
C
C
C
22
22
22
N
The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop
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
G
4
A
N1
G
4
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
19
A
N4
C
19
1_555
hydrog
TYPE_8_PAIR
A
G
5
A
N1
G
5
1_555
A
A
16
A
N1
A
16
1_555
hydrog
TYPE_8_PAIR
A
G
5
A
O6
G
5
1_555
A
A
16
A
N6
A
16
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
A
G
15
A
N1
G
15
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
A
G
15
A
O6
G
15
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
A
G
15
A
N2
G
15
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
A
C
14
A
N4
C
14
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
13
A
N1
G
13
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
13
A
O6
G
13
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
13
A
N2
G
13
1_555
hydrog
U-G MISPAIR
A
U
9
A
O2
U
9
1_555
A
G
12
A
N1
G
12
1_555
hydrog
G-G MISPAIR
A
G
12
A
N2
G
12
1_555
A
G
13
A
N3
G
13
1_555
RNA
RNA
1OSW
PDB
1
1OSW
1
23
1OSW
1
23
1OSW
A
1
1
23