0.043860
0.000000
0.000000
0.000000
0.043860
0.000000
0.000000
0.000000
0.006109
0.00000
0.00000
0.00000
Safaee, N.
Noronha, A.M.
Kozlov, G.
Rodionov, D.
Wilds, C.J.
Sheldrick, G.M.
Gehring, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
22.800
22.800
163.700
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
H4 N 1
18.038
AMMONIUM ION
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
H
N
40
N
H
N
41
N
N
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
GE
Angew.Chem.Int.Ed.Engl.
9999
1433-7851
52
10370
10373
10.1002/anie.201303461
23813654
Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction.
2013
10.2210/pdb4jrd/pdb
pdb_00004jrd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
100
1
100
1
100
1
FOCUSING MIRRORS
CCD
2010-05-29
MARMOSAIC 300 mm CCD
FOCUSING MIRRORS
CCD
2010-10-21
ADSC QUANTUM 210
FOCUSING MIRRORS
CCD
2010-10-21
ADSC QUANTUM 210
FOCUSING MIRRORS
CCD
2010-10-21
ADSC QUANTUM 210
SI 111 DOUBLE
SINGLE WAVELENGTH
M
x-ray
1
Horizontal focusing 5.05 asymmetric cut Si(111)
SINGLE WAVELENGTH
M
x-ray
1
Horizontal focusing 5.05 asymmetric cut Si(111)
SINGLE WAVELENGTH
M
x-ray
1
Horizontal focusing 5.05 asymmetric cut Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.977
1.0
0.987
1.0
08ID-1
CLSI
0.977
SYNCHROTRON
CLSI BEAMLINE 08ID-1
A1
CHESS
0.987
SYNCHROTRON
CHESS BEAMLINE A1
A1
CHESS
0.987
SYNCHROTRON
CHESS BEAMLINE A1
A1
CHESS
0.987
SYNCHROTRON
CHESS BEAMLINE A1
3576.306
RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
2
syn
polymer
18.038
AMMONIUM ION
18
syn
non-polymer
18.015
water
76
nat
water
no
no
AAAAAAAAAAA
AAAAAAAAAAA
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
5
1.49
17.29
VAPOR DIFFUSION, SITTING DROP
RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K
294
-13.408
8
2
A
2
B
1
-179.467
A_A2:A1_B
1
4.781
-6.182
-0.025
5.025
-10.282
8
2
A
3
B
2
-179.334
A_A3:A2_B
2
3.293
-6.071
-0.335
5.012
5.218
8
2
A
4
B
3
179.914
A_A4:A3_B
3
-10.155
6.228
0.020
-4.982
2.843
8
2
A
5
B
4
179.150
A_A5:A4_B
4
-11.912
6.173
0.102
-5.037
-0.083
8
2
A
6
B
5
-179.982
A_A6:A5_B
5
12.517
-6.191
0.080
5.006
3.242
8
2
A
7
B
6
-176.770
A_A7:A6_B
6
13.478
-6.156
0.057
5.094
0.631
8
2
A
8
B
7
-179.556
A_A8:A7_B
7
14.220
-6.001
-0.025
5.151
-2.264
8
2
A
9
B
8
179.228
A_A9:A8_B
8
-15.216
6.110
-0.051
-5.056
4.937
8
2
A
10
B
9
-179.243
A_A10:A9_B
9
13.390
-6.191
-0.033
4.996
0.116
8
2
A
11
B
10
-178.911
A_A11:A10_B
10
5.294
-6.148
0.102
5.017
3.191
33.652
A
A
2
3
7.702
B
B
1
2
3.491
4.432
-0.079
-1.754
AA_A2A3:A2A1_BB
1
4.899
-8.514
33.016
-3.776
0.961
3.812
-138.988
A
A
3
4
1.934
B
B
2
3
3.817
-3.624
0.025
-0.462
AA_A3A4:A3A2_BB
2
0.081
0.043
-138.966
0.271
0.014
3.735
41.604
A
A
4
5
2.128
B
B
3
4
3.750
1.511
0.165
-0.403
AA_A4A5:A4A3_BB
3
0.341
-0.480
41.576
-0.751
-0.191
3.783
-136.306
A
A
5
6
-0.716
B
B
4
5
3.780
1.330
0.287
-0.515
AA_A5A6:A5A4_BB
4
-1.113
-0.599
-136.301
0.268
0.146
3.761
41.129
A
A
6
7
0.271
B
B
5
6
3.764
0.191
0.238
-0.441
AA_A6A7:A6A5_BB
5
-0.199
0.283
41.128
-0.651
-0.364
3.807
45.127
A
A
7
8
0.967
B
B
6
7
3.811
0.742
-0.151
0.078
AA_A7A8:A7A6_BB
6
1.084
-1.413
45.108
0.025
0.310
3.828
-139.077
A
A
8
9
0.141
B
B
7
8
3.827
-0.264
-0.224
-0.024
AA_A8A9:A8A7_BB
7
0.426
0.227
-139.076
0.014
-0.117
3.778
-138.297
A
A
9
10
-0.371
B
B
8
9
3.778
0.693
-0.362
0.231
AA_A9A10:A9A8_BB
8
0.234
0.125
-138.296
-0.128
-0.192
3.565
40.074
A
A
10
11
-1.667
B
B
9
10
3.563
-1.142
-0.134
-0.036
AA_A10A11:A10A9_BB
9
-0.878
1.282
40.050
0.089
0.086
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
1
0
2013-06-05
1
1
2015-08-12
1
2
2024-02-28
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-03-21
REL
REL
NH4
AMMONIUM ION
HOH
water
NH4
101
2
NH4
NH4
101
A
NH4
102
2
NH4
NH4
102
A
NH4
103
2
NH4
NH4
103
A
NH4
104
2
NH4
NH4
104
A
NH4
105
2
NH4
NH4
105
A
NH4
106
2
NH4
NH4
106
A
NH4
107
2
NH4
NH4
107
A
NH4
108
2
NH4
NH4
108
A
NH4
109
2
NH4
NH4
109
A
NH4
110
2
NH4
NH4
110
A
NH4
111
2
NH4
NH4
111
A
NH4
101
2
NH4
NH4
101
B
NH4
102
2
NH4
NH4
102
B
NH4
103
2
NH4
NH4
103
B
NH4
104
2
NH4
NH4
104
B
NH4
105
2
NH4
NH4
105
B
NH4
106
2
NH4
NH4
106
B
NH4
107
2
NH4
NH4
107
B
HOH
201
3
HOH
HOH
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
201
3
HOH
HOH
201
B
HOH
202
3
HOH
HOH
202
B
HOH
203
3
HOH
HOH
203
B
HOH
204
3
HOH
HOH
204
B
HOH
205
3
HOH
HOH
205
B
HOH
206
3
HOH
HOH
206
B
HOH
207
3
HOH
HOH
207
B
HOH
208
3
HOH
HOH
208
B
HOH
209
3
HOH
HOH
209
B
HOH
210
3
HOH
HOH
210
B
HOH
211
3
HOH
HOH
211
B
HOH
212
3
HOH
HOH
212
B
HOH
213
3
HOH
HOH
213
B
HOH
214
3
HOH
HOH
214
B
HOH
215
3
HOH
HOH
215
B
HOH
216
3
HOH
HOH
216
B
HOH
217
3
HOH
HOH
217
B
HOH
218
3
HOH
HOH
218
B
HOH
219
3
HOH
HOH
219
B
HOH
220
3
HOH
HOH
220
B
HOH
221
3
HOH
HOH
221
B
HOH
222
3
HOH
HOH
222
B
HOH
223
3
HOH
HOH
223
B
HOH
224
3
HOH
HOH
224
B
HOH
225
3
HOH
HOH
225
B
HOH
226
3
HOH
HOH
226
B
HOH
227
3
HOH
HOH
227
B
HOH
228
3
HOH
HOH
228
B
HOH
229
3
HOH
HOH
229
B
HOH
230
3
HOH
HOH
230
B
HOH
231
3
HOH
HOH
231
B
HOH
232
3
HOH
HOH
232
B
HOH
233
3
HOH
HOH
233
B
HOH
234
3
HOH
HOH
234
B
HOH
235
3
HOH
HOH
235
B
HOH
236
3
HOH
HOH
236
B
HOH
237
3
HOH
HOH
237
B
HOH
238
3
HOH
HOH
238
B
HOH
239
3
HOH
HOH
239
B
HOH
240
3
HOH
HOH
240
B
HOH
241
3
HOH
HOH
241
B
HOH
242
3
HOH
HOH
242
B
A
1
n
1
A
1
A
A
2
n
2
A
2
A
A
3
n
3
A
3
A
A
4
n
4
A
4
A
A
5
n
5
A
5
A
A
6
n
6
A
6
A
A
7
n
7
A
7
A
A
8
n
8
A
8
A
A
9
n
9
A
9
A
A
10
n
10
A
10
A
A
11
n
11
A
11
A
A
1
n
1
A
1
B
A
2
n
2
A
2
B
A
3
n
3
A
3
B
A
4
n
4
A
4
B
A
5
n
5
A
5
B
A
6
n
6
A
6
B
A
7
n
7
A
7
B
A
8
n
8
A
8
B
A
9
n
9
A
9
B
A
10
n
10
A
10
B
A
11
n
11
A
11
B
0.120
0.128
0.118
0.126
0.151
0.158
986
1152
5.260
5.010
18730
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
HOH
225
U
HOH
1
B
HOH
217
V
HOH
1
A
A
1
0.079
SIDE CHAIN
1
A
A
3
0.067
SIDE CHAIN
1
A
A
4
0.055
SIDE CHAIN
1
A
A
7
0.053
SIDE CHAIN
1
A
A
9
0.055
SIDE CHAIN
1
B
A
4
0.084
SIDE CHAIN
1
B
A
11
0.056
SIDE CHAIN
1
4.90
0.50
129.30
134.20
A
A
A
N1
C2
N3
A
A
A
3
3
3
N
0.158
0.118
0.126
1.00
41.00
5165
1152
23042
22972
6773
5.010
92.6
RANDOM
1,2,3,4
FREE R
1.000
AB INITIO PHASING
BABINET
0
242.00
571.00
1.00
41.00
76
572
18
478
0
0.007
0.021
0.038
0.021
0.005
0.015
0.100
1.000
41.000
4JRD
23042
22972
4
-3.000
0.09440
1,2,3,4
34.3500
2.730
92.6
0.14190
1.00
1.10
4.720
1,2,3,4
1.20
73.1
data collection
MxDC
phasing
SHELXD
refinement
SHELXL
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of the parallel double-stranded helix of poly(A) RNA
1
N
N
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
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
hydrog
TYPE_2_PAIR
A
A
2
A
N6
A
2
1_555
B
A
1
B
N7
A
1
1_555
hydrog
TYPE_2_PAIR
A
A
2
A
N7
A
2
1_555
B
A
1
B
N6
A
1
1_555
hydrog
TYPE_2_PAIR
A
A
3
A
N6
A
3
1_555
B
A
2
B
N7
A
2
1_555
hydrog
TYPE_2_PAIR
A
A
3
A
N7
A
3
1_555
B
A
2
B
N6
A
2
1_555
hydrog
TYPE_2_PAIR
A
A
4
A
N6
A
4
1_555
B
A
3
B
N7
A
3
1_555
hydrog
TYPE_2_PAIR
A
A
4
A
N7
A
4
1_555
B
A
3
B
N6
A
3
1_555
hydrog
TYPE_2_PAIR
A
A
5
A
N6
A
5
1_555
B
A
4
B
N7
A
4
1_555
hydrog
TYPE_2_PAIR
A
A
5
A
N7
A
5
1_555
B
A
4
B
N6
A
4
1_555
hydrog
TYPE_2_PAIR
A
A
6
A
N6
A
6
1_555
B
A
5
B
N7
A
5
1_555
hydrog
TYPE_2_PAIR
A
A
6
A
N7
A
6
1_555
B
A
5
B
N6
A
5
1_555
hydrog
TYPE_2_PAIR
A
A
7
A
N6
A
7
1_555
B
A
6
B
N7
A
6
1_555
hydrog
TYPE_2_PAIR
A
A
7
A
N7
A
7
1_555
B
A
6
B
N6
A
6
1_555
hydrog
TYPE_2_PAIR
A
A
8
A
N6
A
8
1_555
B
A
7
B
N7
A
7
1_555
hydrog
TYPE_2_PAIR
A
A
8
A
N7
A
8
1_555
B
A
7
B
N6
A
7
1_555
hydrog
TYPE_2_PAIR
A
A
9
A
N6
A
9
1_555
B
A
8
B
N7
A
8
1_555
hydrog
TYPE_2_PAIR
A
A
9
A
N7
A
9
1_555
B
A
8
B
N6
A
8
1_555
hydrog
TYPE_2_PAIR
A
A
10
A
N6
A
10
1_555
B
A
9
B
N7
A
9
1_555
hydrog
TYPE_2_PAIR
A
A
10
A
N7
A
10
1_555
B
A
9
B
N6
A
9
1_555
hydrog
TYPE_2_PAIR
A
A
11
A
N6
A
11
1_555
B
A
10
B
N7
A
10
1_555
hydrog
TYPE_2_PAIR
A
A
11
A
N7
A
11
1_555
B
A
10
B
N6
A
10
1_555
RNA
PARALLEL DOUBLE HELIX, POLY(A), MRNA, PABP, Poly(A) motif, RNA
4JRD
PDB
1
4JRD
1
11
4JRD
1
11
4JRD
A
1
1
11
1
11
4JRD
1
11
4JRD
B
1
1
11
BINDING SITE FOR RESIDUE NH4 A 101
A
NH4
101
Software
3
BINDING SITE FOR RESIDUE NH4 A 102
A
NH4
102
Software
4
BINDING SITE FOR RESIDUE NH4 A 103
A
NH4
103
Software
4
BINDING SITE FOR RESIDUE NH4 A 104
A
NH4
104
Software
6
BINDING SITE FOR RESIDUE NH4 A 105
A
NH4
105
Software
4
BINDING SITE FOR RESIDUE NH4 A 106
A
NH4
106
Software
1
BINDING SITE FOR RESIDUE NH4 A 107
A
NH4
107
Software
5
BINDING SITE FOR RESIDUE NH4 A 108
A
NH4
108
Software
5
BINDING SITE FOR RESIDUE NH4 A 109
A
NH4
109
Software
5
BINDING SITE FOR RESIDUE NH4 A 110
A
NH4
110
Software
5
BINDING SITE FOR RESIDUE NH4 A 111
A
NH4
111
Software
4
BINDING SITE FOR RESIDUE NH4 B 101
B
NH4
101
Software
4
BINDING SITE FOR RESIDUE NH4 B 102
B
NH4
102
Software
5
BINDING SITE FOR RESIDUE NH4 B 103
B
NH4
103
Software
6
BINDING SITE FOR RESIDUE NH4 B 104
B
NH4
104
Software
6
BINDING SITE FOR RESIDUE NH4 B 105
B
NH4
105
Software
5
BINDING SITE FOR RESIDUE NH4 B 106
B
NH4
106
Software
5
BINDING SITE FOR RESIDUE NH4 B 107
B
NH4
107
Software
5
A
A
2
A
A
2
3
1_555
A
A
3
A
A
3
3
1_555
B
A
2
B
A
2
3
1_555
A
A
3
A
A
3
4
1_555
A
A
4
A
A
4
4
1_555
A
A
11
A
A
11
4
7_645
B
A
3
B
A
3
4
1_555
A
A
6
A
A
6
4
1_555
A
A
7
A
A
7
4
1_555
A
HOH
216
U
HOH
4
7_655
B
A
6
B
A
6
4
1_555
A
A
5
A
A
5
6
7_545
A
A
9
A
A
9
6
1_555
A
A
10
A
A
10
6
1_555
B
A
9
B
A
9
6
1_555
B
A
10
B
A
10
6
1_555
B
NH4
103
P
NH4
6
7_545
A
A
4
A
A
4
4
7_545
A
A
10
A
A
10
4
1_555
A
A
11
A
A
11
4
1_555
B
A
10
B
A
10
4
1_555
A
A
11
A
A
11
1
1_555
A
A
7
A
A
7
5
1_555
A
A
8
A
A
8
5
1_555
A
HOH
213
U
HOH
5
7_555
B
A
7
B
A
7
5
1_555
B
A
8
B
A
8
5
1_555
A
A
8
A
A
8
5
1_555
A
A
9
A
A
9
5
1_555
A
HOH
233
U
HOH
5
1_555
B
A
8
B
A
8
5
1_555
B
A
9
B
A
9
5
1_555
A
A
4
A
A
4
5
1_555
A
A
5
A
A
5
5
1_555
A
HOH
234
U
HOH
5
1_555
B
A
4
B
A
4
5
1_555
B
A
5
B
A
5
5
1_555
A
A
7
A
A
7
5
1_555
A
A
8
A
A
8
5
1_555
A
HOH
227
U
HOH
5
1_555
B
A
5
B
A
5
5
1_555
B
A
6
B
A
6
5
1_555
A
A
10
A
A
10
4
1_555
A
A
11
A
A
11
4
1_555
B
A
8
B
A
8
4
1_555
B
A
9
B
A
9
4
1_555
A
A
1
A
A
1
4
3_645
A
A
11
A
A
11
4
1_555
B
A
9
B
A
9
4
1_555
B
A
10
B
A
10
4
1_555
A
A
3
A
A
3
5
1_555
A
A
4
A
A
4
5
1_555
B
A
1
B
A
1
5
1_555
B
A
2
B
A
2
5
1_555
B
HOH
201
V
HOH
5
1_555
A
A
5
A
A
5
6
1_555
A
A
6
A
A
6
6
1_555
A
A
9
A
A
9
6
7_655
A
NH4
104
F
NH4
6
7_655
B
A
5
B
A
5
6
1_555
B
A
6
B
A
6
6
1_555
A
A
9
A
A
9
6
1_555
A
A
10
A
A
10
6
1_555
B
A
5
B
A
5
6
7_645
B
A
7
B
A
7
6
1_555
B
A
8
B
A
8
6
1_555
B
HOH
213
V
HOH
6
7_645
A
A
4
A
A
4
5
1_555
A
A
5
A
A
5
5
1_555
B
A
2
B
A
2
5
1_555
B
A
3
B
A
3
5
1_555
B
HOH
204
V
HOH
5
7_555
A
A
6
A
A
6
5
1_555
A
A
7
A
A
7
5
1_555
B
A
4
B
A
4
5
1_555
B
A
5
B
A
5
5
1_555
B
HOH
210
V
HOH
5
7_545
A
A
5
A
A
5
5
1_555
A
A
6
A
A
6
5
1_555
B
A
3
B
A
3
5
1_555
B
A
4
B
A
4
5
1_555
B
HOH
214
V
HOH
5
1_555
92
P 41 21 2