1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Newby, M.I.
Greenbaum, N.L.
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
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
9
958
965
10.1038/nsb873
12426583
Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine
2002
10.2210/pdb1lmv/pdb
pdb_00001lmv
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
unmodified U2 snRNA. Region of U2 snRNA that pairs with the intron branch site during spliceosome assembly (nucleotides 34-39 in yeast U2 snRNA).
2912.775
5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3'
1
nat
polymer
Intron branch site sequence. Region of the pre-mRNA intron that contains the conserved branch site sequence, and pairs with U2 snRNA during spliceosome assembly.
3104.925
5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'
1
nat
polymer
no
no
GGUGUAGUA
GGUGUAGUA
A
polyribonucleotide
no
no
UACUAACACC
UACUAACACC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
sample
4932
Saccharomyces cerevisiae
baker's yeast
Saccharomyces
sample
4932
Saccharomyces cerevisiae
-25.496
1
19
A
1
B
10
0.826
A_G1:C10_B
1
-12.442
-0.772
-0.612
-0.120
-6.382
1
19
A
2
B
9
0.803
A_G2:C9_B
2
-5.566
-0.728
0.067
-0.098
5.406
1
20
A
3
B
8
-8.241
A_U3:A8_B
3
-21.561
-0.690
-0.053
0.013
5.166
1
19
A
4
B
7
-0.983
A_G4:C7_B
4
-16.490
-0.565
0.606
-0.207
11.833
1
A
5
B
6
15.962
A_U5:A6_B
5
-25.806
-0.180
1.028
0.036
1.241
1
20
A
6
B
4
2.161
A_A6:U4_B
6
-0.033
0.274
0.047
0.002
1.594
1
19
A
7
B
3
-2.768
A_G7:C3_B
7
-14.611
-0.659
-0.093
-0.218
6.883
1
20
A
8
B
2
-2.411
A_U8:A2_B
8
-19.409
-0.487
-0.372
-0.023
1.753
1
20
A
9
B
1
3.680
A_A9:U1_B
9
-1.678
0.188
0.287
-0.039
2.739
28.186
A
A
1
2
-0.174
B
B
10
9
2.732
-0.085
-0.199
-0.983
AA_G1G2:C9C10_BB
1
-3.347
6.889
27.991
-2.001
-0.248
2.754
32.497
A
A
2
3
6.039
B
B
9
8
2.899
3.373
-0.744
-1.005
AA_G2U3:A8C9_BB
2
1.176
-2.105
32.306
-2.308
1.508
2.193
36.966
A
A
3
4
22.135
B
B
8
7
2.921
13.668
0.547
-1.167
AA_U3G4:C7A8_BB
3
-5.614
9.091
33.979
-3.346
-1.481
2.799
34.661
A
A
4
5
2.322
B
B
7
6
2.899
1.382
0.805
-1.143
AA_G4U5:A6C7_BB
4
-2.117
3.556
34.571
-2.104
-1.635
4.663
55.450
A
A
5
6
2.182
B
B
6
4
5.611
1.991
1.684
-1.611
AA_U5A6:U4A6_BB
5
-20.008
21.930
51.947
-1.922
-3.719
3.175
28.284
A
A
6
7
0.483
B
B
4
3
3.223
0.236
-0.756
-1.853
AA_A6G7:C3U4_BB
6
1.167
-2.389
28.260
-3.846
1.813
2.871
35.001
A
A
7
8
1.593
B
B
3
2
2.908
0.958
-0.031
-1.339
AA_G7U8:A2C3_BB
7
0.644
-1.071
34.983
-2.353
0.138
2.353
37.639
A
A
8
9
21.332
B
B
2
1
3.101
13.375
0.204
-1.289
AA_U8A9:U1A2_BB
8
-8.049
12.837
34.357
-3.519
-1.231
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
2002-11-27
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine
SEQUENCE
Position 35 in U2 snRNA sequences from S.
cerevisiae is a pseudouridine. This corresponds
to position 5 on strand A, which is a uridine in
1LMV, and a pseudouridine in 1LPW.
RCSB
Y
RCSB
2002-05-02
REL
REL
This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times to assess the buildup rate of each NOE, thereby resolving some of the spectral overlap.
structures with the lowest energy
300
10
2D NOESY
2D NOESY
2D TOCSY
DQF-COSY
50mM sodium chloride
6.4
ambient
278
K
50mM sodium chloride
6.4
ambient
293
K
torsion angle molecular dynamics, followed by congugate gradient minimization
2
lowest energy
1mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA
90% H2O/10% D2O
1mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA
100% D2O
Varian, Inc.
collection
VNMR
5.3
T.D. Goddard and D.G. Kneller
data analysis
Sparky
3.69
Brunger
structure solution
X-PLOR
3.851
Brunger
refinement
X-PLOR
3.851
720
Varian
UNITYPLUS
G
1
n
1
G
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
G
4
n
4
G
4
A
U
5
n
5
U
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
U
8
n
8
U
8
A
A
9
n
9
A
9
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
A
8
n
8
A
8
B
C
9
n
9
C
9
B
C
10
n
10
C
10
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
4.46
0.70
108.50
112.96
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
1
4.57
0.70
108.50
113.07
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
1
4.63
0.70
108.50
113.13
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
1
5.57
0.70
108.50
114.07
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
1
4.96
0.70
108.50
113.46
B
B
B
O4'
C1'
N9
A
A
A
2
2
2
N
1
4.66
0.70
108.50
113.16
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
1
5.29
0.70
108.50
113.79
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
1
5.07
0.70
108.50
113.57
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
1
5.57
0.70
108.50
114.07
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
1
6.30
0.70
108.50
114.80
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
2
4.83
0.70
108.50
113.33
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
2
4.96
0.70
108.50
113.46
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
2
4.93
0.70
108.50
113.43
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
2
4.35
0.70
108.50
112.85
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
2
4.56
0.70
108.50
113.06
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
2
4.73
0.70
108.50
113.23
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
2
5.21
0.70
108.50
113.71
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
2
5.78
0.70
108.50
114.28
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
2
5.61
0.70
108.50
114.11
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
2
6.03
0.70
108.50
114.53
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
2
5.94
0.70
108.50
114.44
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
3
4.98
0.70
108.50
113.48
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
3
5.03
0.70
108.50
113.53
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
3
4.72
0.70
108.50
113.22
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
3
5.80
0.70
108.50
114.30
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
3
4.27
0.70
108.50
112.77
B
B
B
O4'
C1'
N9
A
A
A
2
2
2
N
3
4.42
0.70
108.50
112.92
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
3
4.98
0.70
108.50
113.48
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
3
5.61
0.70
108.50
114.11
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
3
4.31
0.70
108.50
112.81
B
B
B
O4'
C1'
N1
C
C
C
9
9
9
N
3
6.19
0.70
108.50
114.69
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
4
4.52
0.70
108.50
113.02
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
4
5.55
0.70
108.50
114.05
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
4
5.10
0.70
108.50
113.60
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
4
5.91
0.70
108.50
114.41
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
4
4.74
0.70
108.50
113.24
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
4
5.21
0.70
108.50
113.71
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
4
4.53
0.70
108.50
113.03
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
4
6.09
0.70
108.50
114.59
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
5
4.37
0.70
108.50
112.87
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
5
4.99
0.70
108.50
113.49
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
5
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
5
-4.47
0.70
101.30
96.83
A
A
A
C3'
C2'
C1'
A
A
A
6
6
6
N
5
4.99
0.70
108.50
113.49
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
5
5.68
0.70
108.50
114.18
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
5
4.76
0.70
108.50
113.26
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
5
5.01
0.70
108.50
113.51
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
5
5.71
0.70
108.50
114.21
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
5
4.36
0.70
108.50
112.86
B
B
B
O4'
C1'
N9
A
A
A
8
8
8
N
5
5.77
0.70
108.50
114.27
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
6
4.29
0.70
108.50
112.79
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
6
4.29
0.70
108.50
112.79
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
6
4.71
0.70
108.50
113.21
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
6
4.56
0.70
108.50
113.06
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
6
5.64
0.70
108.50
114.14
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
6
4.32
0.70
108.50
112.82
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
6
5.15
0.70
108.50
113.65
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
6
5.13
0.70
108.50
113.63
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
6
5.47
0.70
108.50
113.97
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
6
5.70
0.70
108.50
114.20
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
7
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
7
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N1
U
U
U
3
3
3
N
7
4.53
0.70
108.50
113.03
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
7
5.53
0.70
108.50
114.03
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
7
4.40
0.70
108.50
112.90
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
7
6.00
0.70
108.50
114.50
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
7
5.00
0.70
108.50
113.50
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
7
5.81
0.70
108.50
114.31
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
7
4.72
0.70
108.50
113.22
B
B
B
O4'
C1'
N9
A
A
A
8
8
8
N
7
5.41
0.70
108.50
113.91
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
8
4.42
0.70
108.50
112.92
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
8
5.21
0.70
108.50
113.71
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
8
5.56
0.70
108.50
114.06
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
8
4.95
0.70
108.50
113.45
B
B
B
O4'
C1'
N9
A
A
A
2
2
2
N
8
5.66
0.70
108.50
114.16
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
8
5.72
0.70
108.50
114.22
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
8
4.26
0.70
108.50
112.76
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
8
4.20
0.70
108.50
112.70
B
B
B
O4'
C1'
N1
C
C
C
9
9
9
N
8
5.77
0.70
108.50
114.27
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
9
4.75
0.70
108.50
113.25
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
9
4.63
0.70
108.50
113.13
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
9
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
U
U
U
8
8
8
N
9
4.63
0.70
108.50
113.13
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
9
4.60
0.70
108.50
113.10
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
9
4.28
0.70
108.50
112.78
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
9
5.10
0.70
108.50
113.60
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
9
4.48
0.70
108.50
112.98
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
9
5.87
0.70
108.50
114.37
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
9
5.63
0.70
108.50
114.13
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
10
4.74
0.70
108.50
113.24
A
A
A
O4'
C1'
N9
A
A
A
9
9
9
N
10
5.68
0.70
108.50
114.18
B
B
B
O4'
C1'
N1
U
U
U
1
1
1
N
10
5.44
0.70
108.50
113.94
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
10
5.23
0.70
108.50
113.73
B
B
B
O4'
C1'
N1
U
U
U
4
4
4
N
10
5.77
0.70
108.50
114.27
B
B
B
O4'
C1'
N9
A
A
A
6
6
6
N
10
5.15
0.70
108.50
113.65
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
10
4.59
0.70
108.50
113.09
B
B
B
O4'
C1'
N1
C
C
C
9
9
9
N
10
5.54
0.70
108.50
114.04
B
B
B
O4'
C1'
N1
C
C
C
10
10
10
N
Solution structure of the unmodified U2 snRNA-intron branch site helix from S. cerevisiae
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
10
B
N3
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
10
B
O2
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
10
B
N4
C
10
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
9
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
9
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
9
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
U
3
A
N3
U
3
1_555
B
A
8
B
N1
A
8
1_555
hydrog
WATSON-CRICK
A
U
3
A
O4
U
3
1_555
B
A
8
B
N6
A
8
1_555
hydrog
G-A MISPAIR
A
G
4
A
O6
G
4
1_555
B
A
6
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
B
C
7
B
N4
C
7
1_555
hydrog
U-A PAIR
A
U
5
A
O4
U
5
1_555
B
A
5
B
N6
A
5
1_555
hydrog
U-A PAIR
A
U
5
A
N3
U
5
1_555
B
A
6
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
A
6
A
N1
A
6
1_555
B
U
4
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
A
6
A
N6
A
6
1_555
B
U
4
B
O4
U
4
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
B
A
2
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
B
A
2
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
A
9
A
N1
A
9
1_555
B
U
1
B
N3
U
1
1_555
hydrog
WATSON-CRICK
A
A
9
A
N6
A
9
1_555
B
U
1
B
O4
U
1
1_555
RNA
U2 snRNA, branch site, solution structure, A-form helix, RNA
1LMV
PDB
1
1LMV
1LMV
PDB
2
1LMV
1
9
1LMV
1
9
1LMV
A
1
1
9
1
10
1LMV
1
10
1LMV
B
2
1
10