1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kruschel, D.
Skilandat, M.
Sigel, R.K.O.
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
UK
Rna
RNARFU
2122
1355-8382
20
295
307
10.1261/rna.041137.113
24448450
NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
2014
10.2210/pdb2m23/pdb
pdb_00002m23
sequence produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase
9301.547
RNA (29-MER)
d3'EBS1
A15C, A17C
1
syn
polymer
2197.355
RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_
IBS1
U61G, U63G
1
syn
polymer
no
no
GGAGUAUGUAUUGGCACUGAGCAUACUCC
GGAGUAUGUAUUGGCACUGAGCAUACUCC
A
polyribonucleotide
no
no
CAGUGUC
CAGUGUC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-9.700
1
19
A
1
A
29
-1.057
A_G1:C29_A
1
-9.138
-0.798
0.171
-0.443
11.612
1
19
A
2
A
28
-4.093
A_G2:C28_A
2
-5.530
-0.812
0.368
-0.436
0.293
1
20
A
3
A
27
-6.436
A_A3:U27_A
3
-6.177
-0.691
0.523
-0.255
0.554
1
19
A
4
A
26
-0.488
A_G4:C26_A
4
-8.675
0.021
-0.048
-0.160
4.514
1
20
A
5
A
25
5.247
A_U5:A25_A
5
-6.690
0.903
-0.358
-0.194
3.613
1
20
A
6
A
24
10.361
A_A6:U24_A
6
-14.363
-0.803
-0.416
-0.325
2.050
1
20
A
7
A
23
-5.836
A_U7:A23_A
7
-7.103
-0.798
-0.125
-0.168
7.161
1
19
A
8
A
22
-4.319
A_G8:C22_A
8
-1.878
0.526
-0.117
0.062
-2.938
1
28
A
9
A
21
3.718
A_U9:G21_A
9
2.429
1.933
0.174
-0.261
15.659
1
20
A
11
A
20
-43.927
A_U11:A20_A
10
-31.892
-1.692
-0.047
0.268
0.420
1
19
B
59
A
19
-0.577
B_C59:G19_A
11
-5.553
-0.511
-0.068
-0.212
7.378
1
20
B
60
A
18
8.537
B_A60:U18_A
12
-9.139
-0.882
0.391
-0.348
-4.398
1
19
B
61
A
17
0.663
B_G61:C17_A
13
-10.763
0.514
-0.187
-0.241
-3.105
1
20
B
62
A
16
-11.908
B_U62:A16_A
14
-11.160
-1.193
-0.108
-0.043
2.179
1
19
B
63
A
15
-3.488
B_G63:C15_A
15
1.891
0.635
-0.240
-0.226
4.845
1
28
B
64
A
14
-8.721
B_U64:G14_A
16
-5.544
1.439
-0.991
-0.543
6.083
1
19
B
65
A
13
9.784
B_C65:G13_A
17
-12.751
-0.498
-0.354
-0.040
2.239
31.564
A
A
1
2
0.852
A
A
29
28
2.160
0.463
-1.366
-1.235
AA_G1G2:C28C29_AA
1
-2.458
4.523
31.468
-2.329
2.204
3.979
35.635
A
A
2
3
1.746
A
A
28
27
4.019
1.068
-0.279
-1.637
AA_G2A3:U27C28_AA
2
-1.758
2.875
35.578
-2.865
0.144
2.668
30.741
A
A
3
4
4.088
A
A
27
26
2.821
2.166
0.176
-2.151
AA_A3G4:C26U27_AA
3
0.268
-0.506
30.666
-4.413
-0.287
2.110
38.426
A
A
4
5
21.261
A
A
26
25
2.783
13.706
-0.207
-1.441
AA_G4U5:A25C26_AA
4
0.751
-1.165
35.977
-3.512
0.387
2.632
24.360
A
A
5
6
16.139
A
A
25
24
3.229
6.718
0.016
-1.720
AA_U5A6:U24A25_AA
5
1.786
-4.291
23.362
-6.003
0.475
3.957
40.110
A
A
6
7
-7.379
A
A
24
23
3.744
-5.036
-1.302
-0.925
AA_A6U7:A23U24_AA
6
-4.979
7.295
39.505
-0.667
1.224
2.944
34.651
A
A
7
8
-0.518
A
A
23
22
2.933
-0.308
0.248
-1.666
AA_U7G8:C22A23_AA
7
-0.430
0.722
34.647
-2.754
-0.476
2.548
42.121
A
A
8
9
21.175
A
A
22
21
3.380
14.917
-0.089
-1.851
AA_G8U9:G21C22_AA
8
0.448
-0.635
39.502
-4.020
0.167
1.336
43.647
A
A
9
11
-25.909
A
A
21
20
5.252
-17.049
-3.594
-0.612
AA_U9U11:A20G21_AA
9
29.017
-44.096
28.204
1.225
8.320
3.445
49.283
A
B
11
59
-12.403
A
A
20
19
3.502
-10.216
1.372
-1.655
AB_U11C59:G19A20_AA
10
-9.598
11.651
47.367
-1.156
-2.424
3.192
30.735
B
B
59
60
-12.973
A
A
19
18
2.855
-6.807
-0.029
-1.937
BB_C59A60:U18G19_AA
11
-3.525
6.718
29.786
-2.401
-0.594
2.196
44.922
B
B
60
61
27.179
A
A
18
17
3.133
20.088
-0.623
-1.380
BB_A60G61:C17U18_AA
12
2.803
-3.792
40.296
-3.378
1.034
1.889
27.659
B
B
61
62
19.540
A
A
17
16
2.748
9.171
-0.969
-2.200
BB_G61U62:A16C17_AA
13
-0.205
0.436
26.121
-6.226
1.990
2.519
40.566
B
B
62
63
19.257
A
A
16
15
3.037
13.127
0.399
-1.130
BB_U62G63:C15A16_AA
14
-1.409
2.068
38.443
-2.910
-0.712
1.786
41.009
B
B
63
64
31.706
A
A
15
14
3.086
21.104
-0.783
-1.416
BB_G63U64:G14C15_AA
15
7.112
-10.685
34.656
-3.896
1.750
0.610
35.986
B
B
64
65
55.192
A
A
14
13
2.770
29.383
0.994
-1.250
BB_U64C65:G13G14_AA
16
-0.552
1.037
21.001
-4.802
-1.661
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Database references
Database references
Data collection
Database references
Other
1
0
2013-12-18
1
1
2014-02-26
1
2
2014-03-12
1
3
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
2014-04-16
SPRSDE
BMRB
Y
RCSB
2012-12-12
REL
REL
REL
REL
4932
Saccharomyces cerevisiae
sample
34
27
36
32
28
28
33
96
747
250
348
82
structures with the lowest energy
200
20
0.2
5
0.2
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D 1H-1H NOESY
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aliphatic
2D 1H-15N HSQC
2D 1H-13C HSQC aromatic
2D 1H-13C HSQC aromatic
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D JNN HNN COSY
1D-31P
F1,2 X-filtered 1H-1H NOESY
F1,2 X-filtered 1H-1H TOCSY
0.5-0.9
mM
0.5-0.9
mM
110
mM
10
uM
0.5-0.9
mM
0.5-0.9
mM
110
mM
10
uM
0.5
mM
[U-100% 13C; U-100% 15N]
0.5
mM
110
mM
10
uM
0.5
mM
[U-100% 13C; U-100% 15N]
0.5
mM
110
mM
10
uM
0.6
mM
[3',4',5',5'',5-100% 2H]
0.6
mM
110
mM
10
uM
0.5
mM
[U-100% 13C; U-100% 15N]
0.5
mM
110
mM
10
uM
25.6
mg/mL
110
6.8
ambient
298
K
110
6.8
ambient
278
K
110
6.8
ambient
293
K
molecular dynamics, torsion angle dynamics
1
lowest energy
0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O
90% H2O/10% D2O
Goddard
chemical shift assignment
Sparky
3.1
Goddard
data analysis
Sparky
3.1
Goddard
peak picking
Sparky
3.1
Bruker Biospin
collection
TopSpin
1.3, 2.0, 2.1
Bruker Biospin
processing
TopSpin
1.3, 2.0, 2.1
Guntert, Braun and Wuthrich
data analysis
DYANA
1.5
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNSSOLVE
1.2
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
2.24
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
2.24
700
Bruker
AVANCE
Bruker Avance
600
Bruker
AVANCE
Bruker Avance
500
Bruker
AVANCE
Bruker Avance
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
U
5
n
5
U
5
A
A
6
n
6
A
6
A
U
7
n
7
U
7
A
G
8
n
8
G
8
A
U
9
n
9
U
9
A
A
10
n
10
A
10
A
U
11
n
11
U
11
A
U
12
n
12
U
12
A
G
13
n
13
G
13
A
G
14
n
14
G
14
A
C
15
n
15
C
15
A
A
16
n
16
A
16
A
C
17
n
17
C
17
A
U
18
n
18
U
18
A
G
19
n
19
G
19
A
A
20
n
20
A
20
A
G
21
n
21
G
21
A
C
22
n
22
C
22
A
A
23
n
23
A
23
A
U
24
n
24
U
24
A
A
25
n
25
A
25
A
C
26
n
26
C
26
A
U
27
n
27
U
27
A
C
28
n
28
C
28
A
C
29
n
29
C
29
A
C
59
n
1
C
59
B
A
60
n
2
A
60
B
G
61
n
3
G
61
B
U
62
n
4
U
62
B
G
63
n
5
G
63
B
U
64
n
6
U
64
B
C
65
n
7
C
65
B
author_and_software_defined_assembly
PISA
2
dimeric
894
-2.8
6209
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
B
O2
HO5'
U
C
12
59
1.52
1
A
A
H2'
O4'
C
C
28
29
1.57
2
A
A
H2'
O4'
C
C
28
29
1.54
3
A
A
H2'
O4'
C
C
28
29
1.51
3
A
B
O2
HO5'
U
C
12
59
1.56
4
A
A
H2'
O4'
C
C
28
29
1.55
5
A
A
H2'
O4'
C
C
28
29
1.58
6
A
A
H2'
O4'
C
C
28
29
1.54
7
A
A
H2'
O4'
C
C
28
29
1.57
9
A
A
H2'
O4'
C
C
28
29
1.59
10
A
A
H2'
O4'
C
C
28
29
1.53
11
A
A
H2'
O4'
C
C
28
29
1.54
13
A
A
H2'
O4'
C
C
28
29
1.58
13
A
B
H1'
O5'
U
C
12
59
1.60
14
A
A
H2'
O4'
C
C
28
29
1.57
15
A
A
H2'
O4'
C
C
28
29
1.53
16
A
B
H1'
O5'
U
C
12
59
1.56
16
A
B
O2
HO5'
U
C
12
59
1.56
16
A
A
H2'
O4'
C
C
28
29
1.60
17
A
B
O2
HO5'
U
C
12
59
1.49
17
A
A
H2'
O4'
C
C
28
29
1.56
17
A
B
H1'
O5'
U
C
12
59
1.57
19
A
A
H2'
O4'
C
C
28
29
1.58
20
A
A
H2'
O4'
C
C
28
29
1.56
lowest energy, model 1
NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1
1
N
N
2
N
N
hydrog
G-C PAIR
A
G
1
A
O6
G
1
1_555
A
C
28
A
N4
C
28
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
29
A
N3
C
29
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
29
A
O2
C
29
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
29
A
N4
C
29
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
28
A
N3
C
28
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
28
A
O2
C
28
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
28
A
N4
C
28
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
U
27
A
N3
U
27
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
27
A
O4
U
27
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
26
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
26
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
U
5
A
N3
U
5
1_555
A
A
25
A
N1
A
25
1_555
hydrog
WATSON-CRICK
A
U
5
A
O4
U
5
1_555
A
A
25
A
N6
A
25
1_555
hydrog
WATSON-CRICK
A
A
6
A
N1
A
6
1_555
A
U
24
A
N3
U
24
1_555
hydrog
WATSON-CRICK
A
A
6
A
N6
A
6
1_555
A
U
24
A
O4
U
24
1_555
hydrog
WATSON-CRICK
A
U
7
A
N3
U
7
1_555
A
A
23
A
N1
A
23
1_555
hydrog
WATSON-CRICK
A
U
7
A
O4
U
7
1_555
A
A
23
A
N6
A
23
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
A
C
22
A
N4
C
22
1_555
hydrog
TYPE_28_PAIR
A
U
9
A
N3
U
9
1_555
A
G
21
A
O6
G
21
1_555
hydrog
TYPE_28_PAIR
A
U
9
A
O2
U
9
1_555
A
G
21
A
N1
G
21
1_555
hydrog
A-A MISPAIR
A
A
10
A
N6
A
10
1_555
A
A
20
A
N1
A
20
1_555
hydrog
WATSON-CRICK
A
U
11
A
N3
U
11
1_555
A
A
20
A
N1
A
20
1_555
hydrog
WATSON-CRICK
A
U
11
A
O4
U
11
1_555
A
A
20
A
N6
A
20
1_555
hydrog
U-A PAIR
A
U
12
A
O4
U
12
1_555
B
A
60
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
G
13
A
N1
G
13
1_555
B
C
65
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
13
A
N2
G
13
1_555
B
C
65
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
13
A
O6
G
13
1_555
B
C
65
B
N4
C
7
1_555
hydrog
TYPE_28_PAIR
A
G
14
A
N1
G
14
1_555
B
U
64
B
O2
U
6
1_555
hydrog
TYPE_28_PAIR
A
G
14
A
O6
G
14
1_555
B
U
64
B
N3
U
6
1_555
hydrog
G-C PAIR
A
G
14
A
N1
G
14
1_555
B
C
65
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
C
15
A
N3
C
15
1_555
B
G
63
B
N1
G
5
1_555
hydrog
WATSON-CRICK
A
C
15
A
N4
C
15
1_555
B
G
63
B
O6
G
5
1_555
hydrog
WATSON-CRICK
A
C
15
A
O2
C
15
1_555
B
G
63
B
N2
G
5
1_555
hydrog
WATSON-CRICK
A
A
16
A
N1
A
16
1_555
B
U
62
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
A
16
A
N6
A
16
1_555
B
U
62
B
O4
U
4
1_555
hydrog
WATSON-CRICK
A
C
17
A
N3
C
17
1_555
B
G
61
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
17
A
N4
C
17
1_555
B
G
61
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
17
A
O2
C
17
1_555
B
G
61
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
U
18
A
N3
U
18
1_555
B
A
60
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
18
A
O4
U
18
1_555
B
A
60
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
G
19
A
N1
G
19
1_555
B
C
59
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
G
19
A
N2
G
19
1_555
B
C
59
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
G
19
A
O6
G
19
1_555
B
C
59
B
N4
C
1
1_555
RNA
group II intron, ribozyme, hairpin, EBS1, IBS1, splicing, 5'-splice site, RNA
2M23
PDB
1
2M23
GGAGUAUGUAUUGGCACUGAGCAUACUCC
2M23
PDB
2
2M23
CAGUGUC
1
29
2M23
1
29
2M23
A
1
1
29
59
65
2M23
59
65
2M23
B
2
1
7