1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Liu, H.
Matsugami, A.
Katahira, M.
Uesugi, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-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
322
955
970
10.1016/S0022-2836(02)00876-8
12367521
A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops
2002
10.2210/pdb1my9/pdb
pdb_00001my9
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
K+ CATION STABILIZED
4599.764
5'-R(*GP*GP*AP*GP*GP*UP*UP*UP*UP*GP*GP*AP*GP*G)-3'
2
syn
polymer
no
no
GGAGGUUUUGGAGG
GGAGGUUUUGGAGG
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-26.724
6
A
11
A
14
-91.374
A_G11:G14_A
1
50.366
1.671
-1.465
2.575
-16.923
3
6
A
1
A
13
101.415
A_G1:G13_A
2
0.605
-0.529
0.328
-3.759
-0.080
A
4
B
27
18.244
A_G4:G27_B
3
34.679
-0.459
2.071
0.412
9.881
3
6
B
15
B
18
-84.126
B_G15:G18_B
4
-3.519
1.015
1.211
3.231
-18.836
6
B
25
B
28
-88.174
B_G25:G28_B
5
31.990
1.684
-1.152
3.206
8.217
6
B
19
B
16
82.301
B_G19:G16_B
6
-20.933
-2.135
-0.086
-3.322
-4.248
63.562
A
A
11
1
16.935
A
A
14
13
-4.341
17.480
-0.796
-1.432
AA_G11G1:G13G14_AA
1
-16.461
15.948
59.297
-0.309
1.745
-1.471
125.870
A
A
1
4
0.151
A
B
13
27
-1.495
0.270
-1.046
-4.148
AA_G1G4:G27G13_BA
2
-6.042
3.393
125.788
-2.328
0.610
-0.029
-172.195
A
B
4
15
84.679
B
B
27
18
-4.499
-164.158
-1.558
1.229
AB_G4G15:G18G27_BB
3
50.265
25.929
-40.454
-2.127
-1.244
-0.474
-176.815
B
B
25
19
4.689
B
B
28
16
-0.479
-9.374
0.603
3.235
BB_G25G19:G16G28_BB
4
14.810
7.408
-176.777
-1.619
0.301
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2003-10-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2002-10-04
REL
structures with the lowest energy
1
2D NOESY
2D NOESY
2D TOCSY
DQF-COSY
16 mM KCl
6.5
ambient
283
K
16 mM KCl
6.5
ambient
305.5
K
simulated annealing
1
lowest energy
1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl
95% H2O/5% D2O
1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl
100% D2O
Brunger
structure solution
X-PLOR
3.851
Brunger
refinement
X-PLOR
3.851
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
U
6
n
6
U
6
A
U
7
n
7
U
7
A
U
8
n
8
U
8
A
U
9
n
9
U
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
A
12
n
12
A
12
A
G
13
n
13
G
13
A
G
14
n
14
G
14
A
G
15
n
1
G
15
B
G
16
n
2
G
16
B
A
17
n
3
A
17
B
G
18
n
4
G
18
B
G
19
n
5
G
19
B
U
20
n
6
U
20
B
U
21
n
7
U
21
B
U
22
n
8
U
22
B
U
23
n
9
U
23
B
G
24
n
10
G
24
B
G
25
n
11
G
25
B
A
26
n
12
A
26
B
G
27
n
13
G
27
B
G
28
n
14
G
28
B
author_defined_assembly
2
dimeric
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
HO2'
OP2
G
G
10
11
1.37
1
A
B
O5'
H1'
G
G
1
18
1.53
1
A
A
O4'
H61
G
A
10
12
1.55
1
A
A
H1'
O4'
G
U
5
6
1.60
1
4.31
0.50
113.10
117.41
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.48
0.40
106.40
103.92
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
3.41
0.50
113.80
117.21
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
-2.61
0.40
105.80
103.19
A
A
A
C8
N9
C4
A
A
A
3
3
3
N
1
4.35
0.50
113.10
117.45
A
A
A
N7
C8
N9
G
G
G
4
4
4
N
1
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
4
4
4
N
1
4.59
0.50
113.10
117.69
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
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
1
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
11
11
11
N
1
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
11
11
11
N
1
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
1
-2.40
0.40
105.80
103.40
A
A
A
C8
N9
C4
A
A
A
12
12
12
N
1
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
13
13
13
N
1
-2.79
0.40
106.40
103.61
A
A
A
C8
N9
C4
G
G
G
13
13
13
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
14
14
14
N
1
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
14
14
14
N
1
4.36
0.50
113.10
117.46
B
B
B
N7
C8
N9
G
G
G
15
15
15
N
1
-2.56
0.40
106.40
103.84
B
B
B
C8
N9
C4
G
G
G
15
15
15
N
1
4.56
0.50
113.10
117.66
B
B
B
N7
C8
N9
G
G
G
16
16
16
N
1
-2.60
0.40
106.40
103.80
B
B
B
C8
N9
C4
G
G
G
16
16
16
N
1
3.46
0.50
113.80
117.26
B
B
B
N7
C8
N9
A
A
A
17
17
17
N
1
-2.58
0.40
105.80
103.22
B
B
B
C8
N9
C4
A
A
A
17
17
17
N
1
4.38
0.50
113.10
117.48
B
B
B
N7
C8
N9
G
G
G
18
18
18
N
1
-2.59
0.40
106.40
103.81
B
B
B
C8
N9
C4
G
G
G
18
18
18
N
1
4.52
0.50
113.10
117.62
B
B
B
N7
C8
N9
G
G
G
19
19
19
N
1
-2.70
0.40
106.40
103.70
B
B
B
C8
N9
C4
G
G
G
19
19
19
N
1
4.40
0.50
113.10
117.50
B
B
B
N7
C8
N9
G
G
G
24
24
24
N
1
-2.59
0.40
106.40
103.81
B
B
B
C8
N9
C4
G
G
G
24
24
24
N
1
4.49
0.50
113.10
117.59
B
B
B
N7
C8
N9
G
G
G
25
25
25
N
1
-2.57
0.40
106.40
103.83
B
B
B
C8
N9
C4
G
G
G
25
25
25
N
1
3.73
0.50
113.80
117.53
B
B
B
N7
C8
N9
A
A
A
26
26
26
N
1
-2.43
0.40
105.80
103.37
B
B
B
C8
N9
C4
A
A
A
26
26
26
N
1
4.47
0.50
113.10
117.57
B
B
B
N7
C8
N9
G
G
G
27
27
27
N
1
-2.66
0.40
106.40
103.74
B
B
B
C8
N9
C4
G
G
G
27
27
27
N
1
4.56
0.50
113.10
117.66
B
B
B
N7
C8
N9
G
G
G
28
28
28
N
1
-2.67
0.40
106.40
103.73
B
B
B
C8
N9
C4
G
G
G
28
28
28
N
Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops
1
N
N
1
N
N
hydrog
TYPE_11_PAIR
A
G
1
A
N2
G
1
1_555
A
A
3
A
N7
A
3
1_555
hydrog
TYPE_11_PAIR
A
G
1
A
N3
G
1
1_555
A
A
3
A
N6
A
3
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N1
G
1
1_555
A
G
4
A
O6
G
4
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N2
G
1
1_555
A
G
4
A
N7
G
4
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
N7
G
1
1_555
A
G
13
A
N2
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
1
A
O6
G
1
1_555
A
G
13
A
N1
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N1
G
2
1_555
A
G
5
A
O6
G
5
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N2
G
2
1_555
A
G
5
A
N7
G
5
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
N7
G
2
1_555
A
G
14
A
N2
G
14
1_555
hydrog
TYPE_6_PAIR
A
G
2
A
O6
G
2
1_555
A
G
14
A
N1
G
14
1_555
hydrog
TYPE_6_PAIR
A
G
4
A
N1
G
4
1_555
A
G
10
A
O6
G
10
1_555
hydrog
TYPE_6_PAIR
A
G
4
A
N2
G
4
1_555
A
G
10
A
N7
G
10
1_555
hydrog
G-G MISPAIR
A
G
4
A
O6
G
4
1_555
B
G
27
B
N1
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
5
A
N1
G
5
1_555
A
G
11
A
O6
G
11
1_555
hydrog
TYPE_6_PAIR
A
G
5
A
N2
G
5
1_555
A
G
11
A
N7
G
11
1_555
hydrog
TYPE_11_PAIR
A
G
10
A
N2
G
10
1_555
A
A
12
A
N7
A
12
1_555
hydrog
TYPE_11_PAIR
A
G
10
A
N3
G
10
1_555
A
A
12
A
N6
A
12
1_555
hydrog
TYPE_6_PAIR
A
G
10
A
N1
G
10
1_555
A
G
13
A
O6
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
10
A
N2
G
10
1_555
A
G
13
A
N7
G
13
1_555
hydrog
TYPE_6_PAIR
A
G
11
A
N1
G
11
1_555
A
G
14
A
O6
G
14
1_555
hydrog
TYPE_6_PAIR
A
G
11
A
N2
G
11
1_555
A
G
14
A
N7
G
14
1_555
hydrog
A-G MISPAIR
A
A
12
A
N6
A
12
1_555
B
G
27
B
N7
G
13
1_555
hydrog
G-A MISPAIR
A
G
13
A
N7
G
13
1_555
B
A
26
B
N6
A
12
1_555
hydrog
TYPE_11_PAIR
B
G
15
B
N2
G
1
1_555
B
A
17
B
N7
A
3
1_555
hydrog
TYPE_11_PAIR
B
G
15
B
N3
G
1
1_555
B
A
17
B
N6
A
3
1_555
hydrog
TYPE_6_PAIR
B
G
15
B
N1
G
1
1_555
B
G
18
B
O6
G
4
1_555
hydrog
TYPE_6_PAIR
B
G
15
B
N2
G
1
1_555
B
G
18
B
N7
G
4
1_555
hydrog
TYPE_6_PAIR
B
G
15
B
N7
G
1
1_555
B
G
27
B
N2
G
13
1_555
hydrog
TYPE_6_PAIR
B
G
15
B
O6
G
1
1_555
B
G
27
B
N1
G
13
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
N1
G
2
1_555
B
G
19
B
O6
G
5
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
N2
G
2
1_555
B
G
19
B
N7
G
5
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
N7
G
2
1_555
B
G
28
B
N2
G
14
1_555
hydrog
TYPE_6_PAIR
B
G
16
B
O6
G
2
1_555
B
G
28
B
N1
G
14
1_555
hydrog
TYPE_6_PAIR
B
G
18
B
N1
G
4
1_555
B
G
24
B
O6
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
18
B
N2
G
4
1_555
B
G
24
B
N7
G
10
1_555
hydrog
TYPE_6_PAIR
B
G
19
B
N1
G
5
1_555
B
G
25
B
O6
G
11
1_555
hydrog
TYPE_6_PAIR
B
G
19
B
N2
G
5
1_555
B
G
25
B
N7
G
11
1_555
hydrog
TYPE_11_PAIR
B
G
24
B
N2
G
10
1_555
B
A
26
B
N7
A
12
1_555
hydrog
TYPE_11_PAIR
B
G
24
B
N3
G
10
1_555
B
A
26
B
N6
A
12
1_555
hydrog
TYPE_6_PAIR
B
G
24
B
N1
G
10
1_555
B
G
27
B
O6
G
13
1_555
hydrog
TYPE_6_PAIR
B
G
24
B
N2
G
10
1_555
B
G
27
B
N7
G
13
1_555
hydrog
TYPE_6_PAIR
B
G
25
B
N1
G
11
1_555
B
G
28
B
O6
G
14
1_555
hydrog
TYPE_6_PAIR
B
G
25
B
N2
G
11
1_555
B
G
28
B
N7
G
14
1_555
RNA
Parallel RNA quadruplex with a loop, Dimer of two quadruplexes, RNA
1MY9
PDB
1
1MY9
1
14
1MY9
1
14
1MY9
A
1
1
14
15
28
1MY9
15
28
1MY9
B
1
1
14