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
the sequence was 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
no
no
GGAGUAUGUAUUGGCACUGAGCAUACUCC
GGAGUAUGUAUUGGCACUGAGCAUACUCC
A
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
-4.707
1
19
A
1
A
29
-2.165
A_G1:C29_A
1
-3.708
-0.746
0.131
-0.380
1.735
1
19
A
2
A
28
0.549
A_G2:C28_A
2
-3.898
-0.773
0.108
-0.328
-7.020
1
20
A
3
A
27
-4.030
A_A3:U27_A
3
1.023
-0.834
-0.218
-0.122
-5.668
1
19
A
4
A
26
0.185
A_G4:C26_A
4
-10.373
0.530
-0.288
-0.213
0.345
1
20
A
5
A
25
12.374
A_U5:A25_A
5
-5.698
0.519
-0.217
-0.320
-0.636
1
20
A
6
A
24
15.510
A_A6:U24_A
6
-14.543
-0.544
-0.298
-0.315
1.034
1
20
A
7
A
23
10.706
A_U7:A23_A
7
-9.337
0.116
-0.483
-0.402
0.601
1
19
A
8
A
22
-6.640
A_G8:C22_A
8
-1.392
0.780
-0.427
-0.189
3.928
1
28
A
9
A
21
-8.674
A_U9:G21_A
9
3.395
1.646
-0.292
-0.160
7.845
1
A
10
A
20
-52.005
A_A10:A20_A
10
-3.090
1.841
-2.450
-0.398
3.368
32.532
A
A
1
2
1.792
A
A
29
28
3.363
1.004
-0.931
-0.709
AA_G1G2:C28C29_AA
1
-1.031
1.842
32.501
-1.446
1.477
4.651
37.906
A
A
2
3
-18.098
A
A
28
27
4.595
-11.576
-0.162
-0.934
AA_G2A3:U27C28_AA
2
2.058
-3.217
36.100
0.712
0.632
2.006
32.035
A
A
3
4
20.895
A
A
27
26
2.751
11.296
0.070
-1.675
AA_A3G4:C26U27_AA
3
0.063
-0.117
30.026
-4.567
-0.117
2.240
35.173
A
A
4
5
22.667
A
A
26
25
2.868
13.370
-0.167
-1.158
AA_G4U5:A25C26_AA
4
-1.258
2.132
32.584
-3.538
0.124
1.964
37.195
A
A
5
6
36.053
A
A
25
24
2.986
21.627
-0.143
-0.852
AA_U5A6:U24A25_AA
5
1.763
-2.939
30.393
-3.754
0.421
3.468
39.814
A
A
6
7
2.828
A
A
24
23
3.516
1.925
-0.120
-0.977
AA_A6U7:A23U24_AA
6
-0.644
0.946
39.765
-1.672
0.097
2.213
35.661
A
A
7
8
19.534
A
A
23
22
2.992
11.742
-1.008
-1.688
AA_U7G8:C22A23_AA
7
2.686
-4.469
33.627
-4.153
1.966
2.313
35.029
A
A
8
9
25.574
A
A
22
21
3.287
14.908
-0.525
-1.488
AA_G8U9:G21C22_AA
8
3.175
-5.446
31.633
-4.498
1.303
2.940
32.935
A
A
9
10
-18.153
A
A
21
20
3.929
-9.959
-2.570
-0.640
AA_U9A10:A20G21_AA
9
10.475
-19.092
29.673
0.752
6.513
repository
Initial release
Database references
Database references
1
0
2013-12-18
1
1
2014-02-26
1
2
2014-03-12
2014-04-16
SPRSDE
BMRB
Y
RCSB
2012-12-12
REL
REL
REL
4932
Saccharomyces cerevisiae
sample
28
16
29
16
16
16
27
48
511
176
250
45
structures with the lowest energy
200
20
0.2
5
0.2
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
2D 1H-15N HSQC
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
2D JNN HNN COSY
2D 1H-1H NOESY
2D 1H-1H NOESY
1D 31P
2D 1H-1H NOESY
2D 1H-13C HSQC
0.4-1.2
mM
10
mM
10
uM
0.4-1.2
mM
10
mM
10
uM
0.7
mM
[U-100% 13C; U-100% 15N]
10
mM
10
uM
0.7
mM
[U-100% 13C; U-100% 15N]
10
mM
10
uM
25.6
mg/mL
0.7
mM
[U-100% 13C; U-100% 15N]
10
mM
10
uM
0.6
mM
[3',4',5',5'',5, 100% 2H]
10
mM
10
uM
10
6.8
ambient
293
K
10
6.8
ambient
278
K
10
6.8
ambient
298
K
10
6.8
ambient
283
K
molecular dynamics, torsion angle dynamics
1
lowest energy
0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O
90% H2O/10% D2O
0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
0.6 mM [3',4',5',5'',5, 100% 2H] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O
100% D2O
Bruker Biospin
collection
TOPSPIN
1.3, 2.0, 2.1
Bruker Biospin
processing
TOPSPIN
1.3, 2.0, 2.1
Goddard
chemical shift assignment
SPARKY
3.1
Goddard
data analysis
SPARKY
3.1
Goddard
peak picking
SPARKY
3.1
Guntert, Braun and Wuthrich
data analysis
DYANA
1.5
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNSSOLVE
1.2
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
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
author_defined_assembly
1
monomeric
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
H3
N1
U
A
7
23
1.56
2
A
A
O2'
H6
A
U
10
11
1.45
2
A
A
O2'
H6
U
U
11
12
1.51
4
A
A
O2'
H6
A
U
10
11
1.45
5
A
A
H4'
O4'
U
G
18
19
1.51
5
A
A
H3
N1
U
A
7
23
1.58
6
A
A
O2'
H6
U
U
11
12
1.44
6
A
A
HO2'
O5'
U
U
11
12
1.51
7
A
A
O2'
H6
U
U
11
12
1.51
8
A
A
H3
N1
U
A
7
23
1.57
8
A
A
O2'
H6
A
U
10
11
1.59
9
A
A
O4
H61
U
A
11
20
1.35
9
A
A
H3
N1
U
A
7
23
1.57
10
A
A
H1
O2'
G
G
13
19
1.41
10
A
A
O2'
H6
A
U
10
11
1.45
10
A
A
H3
N1
U
A
11
20
1.59
11
A
A
O2'
H6
U
U
11
12
1.47
11
A
A
O2'
H5'
G
A
19
20
1.49
12
A
A
HO2'
O5'
C
A
15
16
1.39
12
A
A
O2'
H6
U
U
11
12
1.54
12
A
A
H3
N1
U
A
7
23
1.56
12
A
A
HO2'
O5'
U
U
11
12
1.59
13
A
A
O2'
H6
A
U
10
11
1.45
13
A
A
O2'
H6
U
U
11
12
1.50
13
A
A
H3
N1
U
A
7
23
1.56
14
A
A
HO2'
O5'
A
U
10
11
1.56
14
A
A
O3'
H8
U
G
18
19
1.57
15
A
A
O2'
H6
A
U
10
11
1.44
15
A
A
O2'
H6
U
U
11
12
1.54
16
A
A
O4
H61
U
A
11
20
1.46
16
A
A
H3
N1
U
A
11
20
1.50
16
A
A
O2'
H6
A
U
10
11
1.59
17
A
A
O3'
H8
U
G
18
19
1.52
18
A
A
O2'
H6
A
U
10
11
1.45
19
A
A
HO2'
O5'
A
U
10
11
1.40
19
A
A
O2'
H6
A
U
10
11
1.49
19
A
A
H3
N1
U
A
7
23
1.56
19
A
A
H4'
O4'
C
A
15
16
1.57
20
A
A
HO2'
O5'
A
U
10
11
1.41
20
A
A
O2'
H6
U
U
11
12
1.50
20
A
A
H3
N1
U
A
7
23
1.55
29-MER
lowest energy, model1
NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
1
N
N
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
G-U MISPAIR
A
G
4
A
N2
G
4
1_555
A
U
27
A
O2
U
27
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
N1
A
10
1_555
A
A
20
A
N6
A
20
1_555
RNA
group II intron, ribozyme, splicing, EBS1, hairpin, RNA
2M24
PDB
1
2M24
GGAGUAUGUAUUGGCACUGAGCAUACUCC
1
29
2M24
1
29
2M24
A
1
1
29