1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kerwood, D.J.
Cavaluzzi, M.J.
Borer, P.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
Na 1
22.990
SODIUM ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
US
Biochemistry
BICHAW
0033
0006-2960
40
14518
14529
10.1021/bi0111909
11724565
Structure of SL4 RNA from the HIV-1 packaging signal.
2001
10.2210/pdb1jtw/pdb
pdb_00001jtw
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
HIV-1 packaging signal SL4 hairpin
5232.183
5'-R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3'
1
syn
polymer
22.990
SODIUM ION
15
syn
non-polymer
no
no
GGGUGCGAGAGCGUCA
GGGUGCGAGAGCGUCA
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-32.151
1
19
A
2
A
15
2.253
A_G2:C15_A
1
-16.133
-0.913
-0.961
-0.107
-12.564
1
28
A
3
A
14
1.659
A_G3:U14_A
2
-6.252
-1.628
0.228
-0.180
-6.356
1
28
A
4
A
13
-3.046
A_U4:G13_A
3
-8.872
1.604
0.555
-0.325
-2.112
1
19
A
5
A
12
0.114
A_G5:C12_A
4
-20.398
-0.145
-0.141
0.013
2.942
1
19
A
6
A
11
-1.132
A_C6:G11_A
5
-18.263
0.967
-0.144
-0.224
38.355
A
7
A
10
-31.848
A_G7:A10_A
6
10.668
7.488
0.924
-5.208
1.894
24.512
A
A
2
3
19.028
A
A
15
14
2.791
7.794
0.236
-1.682
AA_G2G3:U14C15_AA
1
-7.880
19.239
21.897
-5.792
-2.405
2.762
42.295
A
A
3
4
13.293
A
A
14
13
3.175
9.515
-0.102
-1.580
AA_G3U4:G13U14_AA
2
-1.135
1.586
41.244
-3.086
0.035
1.244
30.665
A
A
4
5
37.027
A
A
13
12
2.879
18.126
-0.259
-1.610
AA_U4G5:C12G13_AA
3
7.247
-14.804
23.765
-5.597
1.510
2.912
38.122
A
A
5
6
10.951
A
A
12
11
3.089
7.113
0.166
-0.718
AA_G5C6:G11C12_AA
4
0.801
-1.233
37.469
-1.933
-0.160
3.239
45.099
A
A
6
7
1.747
A
A
11
10
2.405
1.324
-3.647
-1.378
AA_C6G7:A10G11_AA
5
-12.449
16.426
43.414
-1.901
3.771
atom_site
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
1
0
2001-12-12
1
1
2008-04-27
1
2
2011-07-13
2
0
2022-02-23
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-08-22
REL
REL
NA
SODIUM ION
This sequence occurs in the packaging signal of HIV-1.
sample
Sodium ions which were distant from the RNA were removed.
structures with the lowest energy
20
14
7.0
K
DYANA structures were further refined with the
molecular dynamics and minimization program, AMBER.
1
closest to the average
~0.7mM SL4 concentration in buffer: 25mM NaCl, 5mM NaHPO4 (pH 7.0), 0.1mM EDTA, 0.01% NaN3
99.96% D2O or 90% H2O, 10% D2O
Wuthrich
refinement
DYANA
1.5
Kollman
structure solution
Amber
5
500
Bruker
AVANCE
600
Bruker
AVANCE
NA
17
2
NA
NA
17
A
NA
18
2
NA
NA
18
A
NA
19
2
NA
NA
19
A
NA
20
2
NA
NA
20
A
NA
21
2
NA
NA
21
A
NA
22
2
NA
NA
22
A
NA
23
2
NA
NA
23
A
NA
24
2
NA
NA
24
A
NA
25
2
NA
NA
25
A
NA
26
2
NA
NA
26
A
NA
27
2
NA
NA
27
A
NA
28
2
NA
NA
28
A
NA
29
2
NA
NA
29
A
NA
30
2
NA
NA
30
A
NA
31
2
NA
NA
31
A
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
G
5
n
5
G
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
A
8
n
8
A
8
A
G
9
n
9
G
9
A
A
10
n
10
A
10
A
G
11
n
11
G
11
A
C
12
n
12
C
12
A
G
13
n
13
G
13
A
U
14
n
14
U
14
A
C
15
n
15
C
15
A
A
16
n
16
A
16
A
author_defined_assembly
1
monomeric
A
G
2
A
OP2
G
2
1_555
A
NA
27
L
NA
NA
1_555
A
G
3
A
OP2
G
3
1_555
146.7
A
G
3
A
O6
G
3
1_555
A
NA
18
C
NA
NA
1_555
A
U
4
A
O4
U
4
1_555
76.5
A
G
3
A
O6
G
3
1_555
A
NA
18
C
NA
NA
1_555
A
G
13
A
O6
G
13
1_555
87.6
A
U
4
A
O4
U
4
1_555
A
NA
18
C
NA
NA
1_555
A
G
13
A
O6
G
13
1_555
79.2
A
G
3
A
O6
G
3
1_555
A
NA
18
C
NA
NA
1_555
A
U
14
A
O4
U
14
1_555
79.7
A
U
4
A
O4
U
4
1_555
A
NA
18
C
NA
NA
1_555
A
U
14
A
O4
U
14
1_555
143.4
A
G
13
A
O6
G
13
1_555
A
NA
18
C
NA
NA
1_555
A
U
14
A
O4
U
14
1_555
72.3
A
G
3
A
OP1
G
3
1_555
A
NA
19
D
NA
NA
1_555
A
U
4
A
OP2
U
4
1_555
148.2
A
U
4
A
OP1
U
4
1_555
A
NA
20
E
NA
NA
1_555
A
U
4
A
O5'
U
4
1_555
52.6
A
U
4
A
OP1
U
4
1_555
A
NA
20
E
NA
NA
1_555
A
G
5
A
OP2
G
5
1_555
149.5
A
U
4
A
O5'
U
4
1_555
A
NA
20
E
NA
NA
1_555
A
G
5
A
OP2
G
5
1_555
97.1
A
G
7
A
OP1
G
7
1_555
A
NA
22
G
NA
NA
1_555
A
G
7
A
OP2
G
7
1_555
52.1
A
G
7
A
OP1
G
7
1_555
A
NA
22
G
NA
NA
1_555
A
A
8
A
OP1
A
8
1_555
134.5
A
G
7
A
OP2
G
7
1_555
A
NA
22
G
NA
NA
1_555
A
A
8
A
OP1
A
8
1_555
149.8
A
A
8
A
OP2
A
8
1_555
A
NA
24
I
NA
NA
1_555
A
G
9
A
OP2
G
9
1_555
116.2
A
G
9
A
OP1
G
9
1_555
A
NA
25
J
NA
NA
1_555
A
G
9
A
O5'
G
9
1_555
50.8
A
G
9
A
OP1
G
9
1_555
A
NA
25
J
NA
NA
1_555
A
A
10
A
OP2
A
10
1_555
152.9
A
G
9
A
O5'
G
9
1_555
A
NA
25
J
NA
NA
1_555
A
A
10
A
OP2
A
10
1_555
102.3
A
G
11
A
OP1
G
11
1_555
A
NA
26
K
NA
NA
1_555
A
G
11
A
OP2
G
11
1_555
56.7
A
G
11
A
O3'
G
11
1_555
A
NA
29
N
NA
NA
1_555
A
C
12
A
OP1
C
12
1_555
56.3
A
C
12
A
OP2
C
12
1_555
A
NA
28
M
NA
NA
1_555
A
G
13
A
OP2
G
13
1_555
148.5
A
U
14
A
OP2
U
14
1_555
A
NA
30
O
NA
NA
1_555
A
U
14
A
O5'
U
14
1_555
51.8
A
U
14
A
OP2
U
14
1_555
A
NA
30
O
NA
NA
1_555
A
C
15
A
OP2
C
15
1_555
147.7
A
U
14
A
O5'
U
14
1_555
A
NA
30
O
NA
NA
1_555
A
C
15
A
OP2
C
15
1_555
96.6
A
C
15
A
O5'
C
15
1_555
A
NA
31
P
NA
NA
1_555
A
A
16
A
OP2
A
16
1_555
102.8
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
13
A
C3'
G
1
WRONG HAND
13
A
C2'
G
1
WRONG HAND
13
A
C4'
G
2
WRONG HAND
13
A
C3'
G
3
WRONG HAND
1
A
G
7
0.073
SIDE CHAIN
1
A
G
11
0.056
SIDE CHAIN
2
A
G
7
0.095
SIDE CHAIN
2
A
C
15
0.063
SIDE CHAIN
3
A
G
7
0.071
SIDE CHAIN
3
A
G
9
0.050
SIDE CHAIN
4
A
G
1
0.057
SIDE CHAIN
4
A
G
7
0.115
SIDE CHAIN
4
A
C
15
0.065
SIDE CHAIN
5
A
G
7
0.079
SIDE CHAIN
5
A
G
9
0.067
SIDE CHAIN
6
A
G
5
0.069
SIDE CHAIN
6
A
G
7
0.049
SIDE CHAIN
7
A
G
2
0.051
SIDE CHAIN
7
A
G
7
0.086
SIDE CHAIN
7
A
G
11
0.064
SIDE CHAIN
8
A
G
5
0.054
SIDE CHAIN
8
A
G
7
0.082
SIDE CHAIN
9
A
G
5
0.060
SIDE CHAIN
9
A
G
7
0.081
SIDE CHAIN
9
A
G
11
0.064
SIDE CHAIN
9
A
C
15
0.080
SIDE CHAIN
10
A
G
2
0.064
SIDE CHAIN
10
A
G
7
0.115
SIDE CHAIN
11
A
G
2
0.057
SIDE CHAIN
11
A
U
4
0.064
SIDE CHAIN
11
A
G
7
0.056
SIDE CHAIN
11
A
C
15
0.094
SIDE CHAIN
12
A
G
7
0.077
SIDE CHAIN
12
A
A
16
0.069
SIDE CHAIN
13
A
G
2
0.058
SIDE CHAIN
13
A
G
7
0.083
SIDE CHAIN
13
A
G
11
0.070
SIDE CHAIN
13
A
C
15
0.085
SIDE CHAIN
14
A
G
5
0.076
SIDE CHAIN
14
A
G
9
0.059
SIDE CHAIN
14
A
A
16
0.086
SIDE CHAIN
3
4.99
0.70
108.50
113.49
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
5
4.37
0.70
108.50
112.87
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
6
5.03
0.70
108.50
113.53
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
8
4.70
0.70
108.50
113.20
A
A
A
O4'
C1'
N1
C
C
C
12
12
12
N
10
4.91
0.70
108.50
113.41
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
10
4.77
0.70
108.50
113.27
A
A
A
O4'
C1'
N1
U
U
U
14
14
14
N
11
4.67
0.70
108.50
113.17
A
A
A
O4'
C1'
N1
C
C
C
6
6
6
N
12
4.62
0.70
108.50
113.12
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
12
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N1
U
U
U
14
14
14
N
12
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N1
C
C
C
15
15
15
N
12
4.95
0.70
108.50
113.45
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
13
6.08
0.70
108.50
114.58
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
13
5.43
0.70
108.50
113.93
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
14
5.17
0.70
108.50
113.67
A
A
A
O4'
C1'
N1
U
U
U
4
4
4
N
14
4.28
0.70
108.50
112.78
A
A
A
O4'
C1'
N1
C
C
C
12
12
12
N
14
4.50
0.70
108.50
113.00
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
Structure of SL4 RNA from the HIV-1 Packaging Signal
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
metalc
2.486
A
G
2
A
OP1
G
2
1_555
A
NA
17
B
NA
NA
1_555
metalc
2.729
A
G
2
A
OP2
G
2
1_555
A
NA
27
L
NA
NA
1_555
metalc
2.617
A
G
3
A
O6
G
3
1_555
A
NA
18
C
NA
NA
1_555
metalc
2.627
A
G
3
A
OP1
G
3
1_555
A
NA
19
D
NA
NA
1_555
metalc
2.621
A
G
3
A
OP2
G
3
1_555
A
NA
27
L
NA
NA
1_555
metalc
2.744
A
U
4
A
O4
U
4
1_555
A
NA
18
C
NA
NA
1_555
metalc
2.536
A
U
4
A
OP2
U
4
1_555
A
NA
19
D
NA
NA
1_555
metalc
2.626
A
U
4
A
OP1
U
4
1_555
A
NA
20
E
NA
NA
1_555
metalc
2.969
A
U
4
A
O5'
U
4
1_555
A
NA
20
E
NA
NA
1_555
metalc
2.679
A
G
5
A
OP2
G
5
1_555
A
NA
20
E
NA
NA
1_555
metalc
2.497
A
C
6
A
OP1
C
6
1_555
A
NA
23
H
NA
NA
1_555
metalc
2.953
A
G
7
A
OP1
G
7
1_555
A
NA
22
G
NA
NA
1_555
metalc
2.845
A
G
7
A
OP2
G
7
1_555
A
NA
22
G
NA
NA
1_555
metalc
2.696
A
A
8
A
OP1
A
8
1_555
A
NA
22
G
NA
NA
1_555
metalc
2.595
A
A
8
A
OP2
A
8
1_555
A
NA
24
I
NA
NA
1_555
metalc
2.559
A
G
9
A
OP2
G
9
1_555
A
NA
24
I
NA
NA
1_555
metalc
2.853
A
G
9
A
OP1
G
9
1_555
A
NA
25
J
NA
NA
1_555
metalc
2.943
A
G
9
A
O5'
G
9
1_555
A
NA
25
J
NA
NA
1_555
metalc
2.620
A
A
10
A
OP2
A
10
1_555
A
NA
25
J
NA
NA
1_555
metalc
2.722
A
G
11
A
OP1
G
11
1_555
A
NA
26
K
NA
NA
1_555
metalc
2.613
A
G
11
A
OP2
G
11
1_555
A
NA
26
K
NA
NA
1_555
metalc
2.619
A
G
11
A
O3'
G
11
1_555
A
NA
29
N
NA
NA
1_555
metalc
2.689
A
C
12
A
OP2
C
12
1_555
A
NA
28
M
NA
NA
1_555
metalc
2.660
A
C
12
A
OP1
C
12
1_555
A
NA
29
N
NA
NA
1_555
metalc
2.592
A
G
13
A
O6
G
13
1_555
A
NA
18
C
NA
NA
1_555
metalc
2.556
A
G
13
A
OP2
G
13
1_555
A
NA
28
M
NA
NA
1_555
metalc
2.901
A
U
14
A
O4
U
14
1_555
A
NA
18
C
NA
NA
1_555
metalc
2.575
A
U
14
A
OP1
U
14
1_555
A
NA
21
F
NA
NA
1_555
metalc
2.664
A
U
14
A
OP2
U
14
1_555
A
NA
30
O
NA
NA
1_555
metalc
2.990
A
U
14
A
O5'
U
14
1_555
A
NA
30
O
NA
NA
1_555
metalc
2.535
A
C
15
A
OP2
C
15
1_555
A
NA
30
O
NA
NA
1_555
metalc
2.893
A
C
15
A
O5'
C
15
1_555
A
NA
31
P
NA
NA
1_555
metalc
2.594
A
A
16
A
OP2
A
16
1_555
A
NA
31
P
NA
NA
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
15
A
N4
C
15
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
N1
G
3
1_555
A
U
14
A
O2
U
14
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
O6
G
3
1_555
A
U
14
A
N3
U
14
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
N3
U
4
1_555
A
G
13
A
O6
G
13
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
O2
U
4
1_555
A
G
13
A
N1
G
13
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
12
A
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
12
A
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
12
A
N4
C
12
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
A
G
11
A
N1
G
11
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
A
G
11
A
O6
G
11
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
A
G
11
A
N2
G
11
1_555
hydrog
G-A MISPAIR
A
G
7
A
N2
G
7
1_555
A
A
10
A
N7
A
10
1_555
RNA
hairpin, tandem G-U pairs, GAGA tetraloops, RNA
1JTW
PDB
1
1JTW
1
16
1JTW
1
16
1JTW
A
1
1
16
BINDING SITE FOR RESIDUE NA A 17
A
NA
17
Software
1
BINDING SITE FOR RESIDUE NA A 18
A
NA
18
Software
4
BINDING SITE FOR RESIDUE NA A 19
A
NA
19
Software
2
BINDING SITE FOR RESIDUE NA A 20
A
NA
20
Software
2
BINDING SITE FOR RESIDUE NA A 21
A
NA
21
Software
2
BINDING SITE FOR RESIDUE NA A 22
A
NA
22
Software
2
BINDING SITE FOR RESIDUE NA A 23
A
NA
23
Software
1
BINDING SITE FOR RESIDUE NA A 24
A
NA
24
Software
3
BINDING SITE FOR RESIDUE NA A 25
A
NA
25
Software
3
BINDING SITE FOR RESIDUE NA A 26
A
NA
26
Software
2
BINDING SITE FOR RESIDUE NA A 27
A
NA
27
Software
2
BINDING SITE FOR RESIDUE NA A 28
A
NA
28
Software
2
BINDING SITE FOR RESIDUE NA A 29
A
NA
29
Software
2
BINDING SITE FOR RESIDUE NA A 30
A
NA
30
Software
2
BINDING SITE FOR RESIDUE NA A 31
A
NA
31
Software
2
A
G
2
A
G
2
1
1_555
A
G
3
A
G
3
4
1_555
A
U
4
A
U
4
4
1_555
A
G
13
A
G
13
4
1_555
A
U
14
A
U
14
4
1_555
A
G
3
A
G
3
2
1_555
A
U
4
A
U
4
2
1_555
A
U
4
A
U
4
2
1_555
A
G
5
A
G
5
2
1_555
A
G
13
A
G
13
2
1_555
A
U
14
A
U
14
2
1_555
A
G
7
A
G
7
2
1_555
A
A
8
A
A
8
2
1_555
A
C
6
A
C
6
1
1_555
A
G
7
A
G
7
3
1_555
A
A
8
A
A
8
3
1_555
A
G
9
A
G
9
3
1_555
A
G
7
A
G
7
3
1_555
A
G
9
A
G
9
3
1_555
A
A
10
A
A
10
3
1_555
A
A
10
A
A
10
2
1_555
A
G
11
A
G
11
2
1_555
A
G
2
A
G
2
2
1_555
A
G
3
A
G
3
2
1_555
A
C
12
A
C
12
2
1_555
A
G
13
A
G
13
2
1_555
A
G
11
A
G
11
2
1_555
A
C
12
A
C
12
2
1_555
A
U
14
A
U
14
2
1_555
A
C
15
A
C
15
2
1_555
A
C
15
A
C
15
2
1_555
A
A
16
A
A
16
2
1_555