0.034783
0.000000
0.001744
0.000000
0.023585
0.000000
0.000000
0.000000
0.030213
0.00000
0.00000
0.00000
Berglund, J.A.
Rosbash, M.
Schultz, S.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
92.87
90.00
28.75
42.40
33.14
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
H2 O
18.015
WATER
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
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
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
H
N
113
N
H
N
114
N
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
N
O
N
124
R
C
N
125
N
O
N
126
R
C
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
C
N
132
N
O
N
133
N
C
N
134
N
C
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
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
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
UK
RNA
RNARFU
2122
1355-8382
7
682
691
10.1017/S1355838201002187
11350032
Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines.
2001
10.2210/pdb1i9x/pdb
pdb_00001i9x
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
Yale mirrors
IMAGE PLATE
1999-02-10
RIGAKU RAXIS IIC
Yale Mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
BPS - U2 SNRNA DUPLEX
4126.509
5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3'
2
syn
polymer
18.015
water
22
nat
water
no
no
UACUAACGUAGUA
UACUAACGUAGUA
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.44
49.68
VAPOR DIFFUSION, HANGING DROP
7.5
MPD, Spermine, Glycerol, tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP
303.0 then shifted to 287.0
MPD
1
Spermine
1
Glycerol
1
tris
1
MPD
2
4.911
1
20
A
1
B
13
7.154
A_U1:A13_B
1
-9.189
-0.365
0.356
-0.092
-1.329
1
20
A
2
B
12
3.879
A_A2:U12_B
2
-17.797
-0.184
0.528
-0.187
-2.820
1
19
A
3
B
11
6.501
A_C3:G11_B
3
-18.735
0.245
0.445
-0.155
0.270
1
20
A
4
B
10
-0.508
A_U4:A10_B
4
-16.122
0.179
0.175
-0.236
-8.766
1
20
A
6
B
9
13.839
A_A6:U9_B
5
-14.060
0.237
-0.458
-0.233
17.448
1
19
A
7
B
8
2.373
A_C7:G8_B
6
-17.470
0.168
-1.059
-0.139
-0.936
1
19
A
8
B
7
6.261
A_G8:C7_B
7
-12.536
-0.350
0.221
0.031
0.295
1
20
A
9
B
6
6.848
A_U9:A6_B
8
-11.272
-0.260
0.262
-0.346
-2.048
1
20
A
10
B
4
-0.311
A_A10:U4_B
9
-9.970
0.355
0.490
-0.225
-3.324
1
19
A
11
B
3
2.488
A_G11:C3_B
10
-16.788
-0.460
0.477
0.013
-5.864
1
20
A
12
B
2
8.348
A_U12:A2_B
11
-13.007
-0.178
0.414
0.059
-3.181
1
20
A
13
B
1
2.172
A_A13:U1_B
12
-6.283
0.286
0.420
-0.086
2.723
35.790
A
A
1
2
17.580
B
B
13
12
3.234
10.620
-0.458
-1.404
AA_U1A2:U12A13_BB
1
-4.709
7.794
33.911
-3.717
0.111
3.154
33.533
A
A
2
3
6.854
B
B
12
11
3.296
3.943
-0.438
-1.233
AA_A2C3:G11U12_BB
2
-2.201
3.826
33.236
-2.779
0.401
2.734
33.161
A
A
3
4
14.937
B
B
11
10
3.100
8.436
-0.600
-1.100
AA_C3U4:A10G11_BB
3
-0.201
0.356
32.098
-3.213
1.021
3.061
41.175
A
A
4
6
13.053
B
B
10
9
3.468
9.109
-0.633
-1.451
AA_U4A6:U9A10_BB
4
1.298
-1.860
40.178
-3.059
1.042
2.394
29.396
A
A
6
7
7.259
B
B
9
8
2.667
3.656
-0.563
-0.951
AA_A6C7:G8U9_BB
5
5.188
-10.301
28.717
-2.488
1.981
1.877
30.574
A
A
7
8
33.605
B
B
8
7
3.755
16.653
1.139
-1.821
AA_C7G8:C7G8_BB
6
-6.202
12.515
24.981
-6.599
-3.332
3.164
31.587
A
A
8
9
2.324
B
B
7
6
3.235
1.265
-0.358
-1.882
AA_G8U9:A6C7_BB
7
-0.495
0.910
31.559
-3.688
0.569
2.824
40.187
A
A
9
10
9.880
B
B
6
4
3.094
6.758
0.495
-1.516
AA_U9A10:U4A6_BB
8
1.431
-2.092
39.613
-2.906
-0.572
2.332
30.598
A
A
10
11
23.893
B
B
4
3
3.136
12.248
0.696
-1.541
AA_A10G11:C3U4_BB
9
3.069
-5.986
27.928
-5.044
-0.787
3.182
33.948
A
A
11
12
6.912
B
B
3
2
3.340
4.024
0.533
-1.420
AA_G11U12:A2C3_BB
10
2.237
-3.843
33.643
-3.078
-0.554
2.446
37.286
A
A
12
13
16.271
B
B
2
1
2.948
10.276
-0.238
-1.455
AA_U12A13:U1A2_BB
11
1.041
-1.649
35.876
-3.421
0.488
diffrn_source
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Data collection
Data collection
Database references
1
0
2001-09-05
1
1
2008-04-27
1
2
2011-07-13
1
3
2018-04-04
1
4
2024-02-07
_diffrn_source.type
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2001-03-21
REL
REL
HOH
water
The UACUAAC is the conserved branchpoint sequence in budding yeast and the GUAGUA is conserved in the U2 snRNP particle.
sample
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
40
2
HOH
HOH
40
A
HOH
41
2
HOH
HOH
41
A
HOH
21
2
HOH
HOH
21
B
HOH
22
2
HOH
HOH
22
B
HOH
23
2
HOH
HOH
23
B
HOH
24
2
HOH
HOH
24
B
HOH
30
2
HOH
HOH
30
B
HOH
31
2
HOH
HOH
31
B
HOH
32
2
HOH
HOH
32
B
HOH
33
2
HOH
HOH
33
B
HOH
37
2
HOH
HOH
37
B
HOH
38
2
HOH
HOH
38
B
HOH
39
2
HOH
HOH
39
B
HOH
42
2
HOH
HOH
42
B
U
1
n
1
U
1
A
A
2
n
2
A
2
A
C
3
n
3
C
3
A
U
4
n
4
U
4
A
A
5
n
5
A
5
A
A
6
n
6
A
6
A
C
7
n
7
C
7
A
G
8
n
8
G
8
A
U
9
n
9
U
9
A
A
10
n
10
A
10
A
G
11
n
11
G
11
A
U
12
n
12
U
12
A
A
13
n
13
A
13
A
U
1
n
1
U
1
B
A
2
n
2
A
2
B
C
3
n
3
C
3
B
U
4
n
4
U
4
B
A
5
n
5
A
5
B
A
6
n
6
A
6
B
C
7
n
7
C
7
B
G
8
n
8
G
8
B
U
9
n
9
U
9
B
A
10
n
10
A
10
B
G
11
n
11
G
11
B
U
12
n
12
U
12
B
A
13
n
13
A
13
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
58
22.18
0.00
12.48
-15.43
0.00
-6.75
Bulk solvent was not used in the refinement.
0.2760000
0.2530000
2.18
8.0
410
4145
3980
96.0
Random
1
Anistropic
THROUGHOUT
0.0
0.0
MIR
G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman,
New Parameters for the Refinement of Nucleic Acid Containing Structures,
Acta Cryst. D, 52, 57-64 (1996).
0.47
0.36
5.0
0.56
0.54
2.18
8.0
22
568
0
546
0
0.005
1.2
12.7
1.49
0.4570000
0.055
0.4270000
2.31
69
93.2
41.4
2.0
30.0
1I9X
4369
4125
0.0
0.0
0.0480000
4.7000000
1
30.1
4.9
96.0
0.3840000
2.18
2.26
2.6
440
27.7000000
4.1
94.0
phasing
MLPHARE
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURE OF BPS-U2 SNRNA DUPLEX
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
U
1
A
N3
U
1
1_555
B
A
13
B
N1
A
13
1_555
hydrog
WATSON-CRICK
A
U
1
A
O4
U
1
1_555
B
A
13
B
N6
A
13
1_555
hydrog
WATSON-CRICK
A
A
2
A
N1
A
2
1_555
B
U
12
B
N3
U
12
1_555
hydrog
WATSON-CRICK
A
A
2
A
N6
A
2
1_555
B
U
12
B
O4
U
12
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
B
G
11
B
N1
G
11
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
11
B
O6
G
11
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
11
B
N2
G
11
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
B
A
10
B
N1
A
10
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
B
A
10
B
N6
A
10
1_555
hydrog
WATSON-CRICK
A
A
6
A
N1
A
6
1_555
B
U
9
B
N3
U
9
1_555
hydrog
WATSON-CRICK
A
A
6
A
N6
A
6
1_555
B
U
9
B
O4
U
9
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
8
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
8
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
8
B
N2
G
8
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
B
C
7
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
U
9
A
N3
U
9
1_555
B
A
6
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
U
9
A
O4
U
9
1_555
B
A
6
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
A
10
A
N1
A
10
1_555
B
U
4
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
A
10
A
N6
A
10
1_555
B
U
4
B
O4
U
4
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
U
12
A
N3
U
12
1_555
B
A
2
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
12
A
O4
U
12
1_555
B
A
2
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
A
13
A
N1
A
13
1_555
B
U
1
B
N3
U
1
1_555
hydrog
WATSON-CRICK
A
A
13
A
N6
A
13
1_555
B
U
1
B
O4
U
1
1_555
RNA
pre-mRNA splicing, bulged adenosine, three helix junction, RNA
1I9X
PDB
1
1I9X
1
13
1I9X
1
13
1I9X
A
1
1
13
1
13
1I9X
1
13
1I9X
B
1
1
13
4
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