1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lynch, S.R.
Puglisi, J.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
306
1023
1035
10.1006/jmbi.2000.4419
11237616
Structure of a eukaryotic decoding region A-site RNA.
2001
10.2210/pdb1fyo/pdb
pdb_00001fyo
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
EUKARYOTIC DECODING REGION A-SITE RNA
8672.185
FRAGMENT OF 18S RIBOSOMAL RNA
18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERS)
U1410A, A1490U
1
syn
polymer
no
no
GGCGUCGCACCUUCGGGUGAAGUCGCC
GGCGUCGCACCUUCGGGUGAAGUCGCC
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
4.468
1
19
A
1
A
27
-10.190
A_G1:C27_A
1
-9.505
-0.346
0.931
-0.585
-7.136
1
19
A
2
A
26
-5.306
A_G2:C26_A
2
5.946
-0.480
-0.105
-0.395
13.771
1
19
A
3
A
25
-3.873
A_C3:G25_A
3
-14.868
0.478
-0.328
-0.382
3.171
1
19
A
4
A
24
-4.379
A_G4:C24_A
4
-21.376
-0.456
0.363
-0.449
1.432
1
16
A
5
A
23
3.734
A_U5:U23_A
5
-14.194
2.921
0.469
-1.905
-12.313
1
19
A
6
A
22
-0.269
A_C6:G22_A
6
-6.295
0.447
-0.700
-0.606
-9.376
1
19
A
8
A
19
-14.271
A_C8:G19_A
7
-14.682
0.244
1.329
-0.768
9.176
1
20
A
9
A
18
-10.898
A_A9:U18_A
8
-11.114
0.215
1.284
-0.376
14.480
1
19
A
10
A
17
-5.277
A_C10:G17_A
9
-9.947
0.328
0.683
-0.418
26.173
1
19
A
11
A
16
-1.800
A_C11:G16_A
10
-19.205
0.595
-0.718
-0.361
-13.698
A
12
A
15
-78.916
A_U12:G15_A
11
-34.618
2.259
0.119
-4.255
-1.160
169.108
A
A
1
2
83.620
A
A
27
26
-0.501
163.230
3.634
-1.123
AA_G1G2:C26C27_AA
1
-3.528
1.807
98.569
-0.257
-1.818
2.725
35.931
A
A
2
3
6.253
A
A
26
25
2.809
3.847
0.344
-0.838
AA_G2C3:G25C26_AA
2
2.781
-4.520
35.626
-1.826
-0.221
2.405
33.642
A
A
3
4
21.482
A
A
25
24
3.235
12.140
0.552
-1.540
AA_C3G4:C24G25_AA
3
-3.804
6.731
31.209
-4.438
-1.511
3.307
51.698
A
A
4
5
-5.918
A
A
24
23
3.242
-5.152
0.357
-1.062
AA_G4U5:U23C24_AA
4
-2.553
2.933
51.399
-0.868
-0.582
2.910
36.784
A
A
5
6
2.664
A
A
23
22
3.325
1.631
-0.087
-1.866
AA_U5C6:G22U23_AA
5
15.613
-25.509
33.372
-3.180
2.271
2.700
33.868
A
A
8
9
-16.431
A
A
19
18
2.348
-9.451
-0.282
-1.611
AA_C8A9:U18G19_AA
6
-0.368
0.639
32.558
-1.566
0.438
3.534
36.589
A
A
9
10
-15.773
A
A
18
17
3.238
-9.783
0.361
-1.511
AA_A9C10:G17U18_AA
7
2.325
-3.748
35.226
-0.985
-0.237
3.084
32.676
A
A
10
11
-11.518
A
A
17
16
2.927
-6.380
0.282
-1.190
AA_C10C11:G16G17_AA
8
7.776
-14.038
31.129
-1.074
0.767
3.271
95.152
A
A
11
12
10.489
A
A
16
15
3.504
15.426
-0.200
-1.409
AA_C11U12:G15G16_AA
9
10.778
-7.328
93.716
-1.241
0.336
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
2001-03-14
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
the eukaryotic decoding region A-site RNA bound to paromomycin
the prokaryotic decoding region A site RNA
the prokaryotic decoding region A site RNA bound to paromomycin
RCSB
Y
RCSB
2000-10-02
REL
This sequence occurs naturally in Tetrahymena thermophila
sample
structures with the least restraint violations,structures with the lowest energy
100
25
2D NOESY
3D_13C-separated_NOESY
3D_15N-separated_NOESY
4D_13C-separated_NOESY
DQF-COSY
10 mM
6.3
1
atm
298
K
682 NOEs, 129 dihedral constraints, 36 Hydrogen bonds
simulated annealing molecular dynamics
12
3 mM decoding site RNA, 13C/15N, 10 mM phosphate pH 6.3, 90% H20/10% D20, 100% D20
90% H2O/10% D20; 100% D2O
Brunger
refinement
X-PLOR
3.83
Brunger
structure solution
X-PLOR
3.83
processing
VNMR
6.1
processing
Felix
6.1
500
Varian
INOVA
800
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
U
5
n
5
U
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
A
9
n
9
A
9
A
C
10
n
10
C
10
A
C
11
n
11
C
11
A
U
12
n
12
U
12
A
U
13
n
13
U
13
A
C
14
n
14
C
14
A
G
15
n
15
G
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
U
18
n
18
U
18
A
G
19
n
19
G
19
A
A
20
n
20
A
20
A
A
21
n
21
A
21
A
G
22
n
22
G
22
A
U
23
n
23
U
23
A
C
24
n
24
C
24
A
G
25
n
25
G
25
A
C
26
n
26
C
26
A
C
27
n
27
C
27
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
O2'
H5''
A
A
20
21
1.41
1
A
A
HO2'
O6
U
G
12
15
1.58
1
A
A
O6
H41
G
C
2
26
1.59
1
A
A
H41
O6
C
G
6
22
1.59
1
A
A
H41
O6
C
G
3
25
1.60
2
A
A
O2'
H5''
A
A
20
21
1.42
2
A
A
HO2'
O6
U
G
12
15
1.58
2
A
A
O6
H41
G
C
1
27
1.59
2
A
A
H41
O6
C
G
6
22
1.60
2
A
A
H41
O6
C
G
3
25
1.60
2
A
A
O6
H41
G
C
2
26
1.60
3
A
A
O2'
H5''
A
A
20
21
1.46
3
A
A
HO2'
O4'
U
C
5
6
1.57
3
A
A
O6
H41
G
C
1
27
1.59
4
A
A
O2'
H5''
A
A
20
21
1.43
4
A
A
O2'
H8
A
A
20
21
1.57
4
A
A
H41
O6
C
G
6
22
1.59
4
A
A
O6
H41
G
C
1
27
1.59
4
A
A
H41
O6
C
G
11
16
1.60
4
A
A
H41
O6
C
G
3
25
1.60
5
A
A
O2'
H5''
A
A
20
21
1.41
5
A
A
H41
O6
C
G
6
22
1.59
5
A
A
O6
H41
G
C
1
27
1.60
6
A
A
O2'
H5''
A
A
20
21
1.44
6
A
A
HO2'
O4'
A
A
20
21
1.45
6
A
A
H41
O6
C
G
3
25
1.58
7
A
A
O2'
H5''
A
A
20
21
1.41
7
A
A
H41
O6
C
G
6
22
1.59
7
A
A
O6
H41
G
C
1
27
1.59
7
A
A
O2'
H8
A
G
21
22
1.60
8
A
A
O2'
H5''
A
A
20
21
1.47
8
A
A
HO2'
O4'
U
C
5
6
1.57
8
A
A
O2'
H8
A
A
20
21
1.58
8
A
A
O6
H41
G
C
1
27
1.59
9
A
A
O2'
H5''
A
A
20
21
1.44
9
A
A
HO2'
O4'
A
A
20
21
1.47
9
A
A
O6
H41
G
C
2
26
1.60
10
A
A
O2'
H5''
A
A
20
21
1.42
10
A
A
O2'
H8
A
A
20
21
1.59
10
A
A
O6
H41
G
C
1
27
1.59
10
A
A
H41
O6
C
G
6
22
1.59
10
A
A
H41
O6
C
G
3
25
1.60
11
A
A
O2'
H5''
A
A
20
21
1.42
11
A
A
H41
O6
C
G
6
22
1.58
11
A
A
O2'
H8
A
A
20
21
1.58
11
A
A
HO2'
O6
U
G
12
15
1.59
12
A
A
O2'
H5''
A
A
20
21
1.44
12
A
A
O6
H41
G
C
1
27
1.59
12
A
A
H41
O6
C
G
11
16
1.60
12
A
A
H41
O6
C
G
3
25
1.60
12
A
A
H41
O6
C
G
6
22
1.60
12
A
A
O2'
H8
A
A
20
21
1.60
13
A
A
O2'
H5''
A
A
20
21
1.44
13
A
A
H41
O6
C
G
6
22
1.59
13
A
A
O2'
H8
A
A
20
21
1.59
13
A
A
O6
H41
G
C
1
27
1.59
13
A
A
H41
O6
C
G
11
16
1.59
14
A
A
O2'
H5''
A
A
20
21
1.41
14
A
A
O6
H41
G
C
1
27
1.60
15
A
A
O2'
H5''
A
A
20
21
1.41
15
A
A
H41
O6
C
G
6
22
1.58
15
A
A
O6
H41
G
C
1
27
1.60
15
A
A
H41
O6
C
G
11
16
1.60
16
A
A
O2'
H5''
A
A
20
21
1.44
16
A
A
HO2'
O4'
A
A
20
21
1.58
16
A
A
O6
H41
G
C
2
26
1.59
17
A
A
O2'
H5''
A
A
20
21
1.41
17
A
A
H41
O6
C
G
6
22
1.58
17
A
A
O2'
H8
A
A
20
21
1.58
17
A
A
O6
H41
G
C
1
27
1.60
17
A
A
O6
H41
G
C
2
26
1.60
18
A
A
O2'
H5''
A
A
20
21
1.44
18
A
A
HO2'
O4'
A
A
20
21
1.54
18
A
A
H41
O6
C
G
6
22
1.58
18
A
A
O6
H41
G
C
1
27
1.60
19
A
A
O2'
H5''
A
A
20
21
1.41
19
A
A
H41
O6
C
G
11
16
1.59
19
A
A
O2'
H8
A
A
20
21
1.59
19
A
A
O6
H41
G
C
1
27
1.60
20
A
A
O2'
H5''
A
A
20
21
1.45
21
A
A
O2'
H5''
A
A
20
21
1.43
21
A
A
O6
H41
G
C
1
27
1.59
21
A
A
H41
O6
C
G
3
25
1.59
21
A
A
O6
H41
G
C
2
26
1.60
22
A
A
O2'
H5''
A
A
20
21
1.44
22
A
A
HO2'
O4'
A
A
20
21
1.51
22
A
A
O6
H41
G
C
1
27
1.59
22
A
A
H41
O6
C
G
6
22
1.59
23
A
A
O2'
H5''
A
A
20
21
1.42
23
A
A
H41
O6
C
G
3
25
1.58
23
A
A
O6
H41
G
C
1
27
1.60
24
A
A
O2'
H5''
A
A
20
21
1.42
24
A
A
O2'
H8
A
G
21
22
1.47
24
A
A
H41
O6
C
G
6
22
1.56
25
A
A
O2'
H5''
A
A
20
21
1.42
25
A
A
O2'
H8
A
A
20
21
1.57
25
A
A
HO2'
O6
U
G
12
15
1.57
25
A
A
H41
O6
C
G
6
22
1.58
25
A
A
HO2'
O4'
G
C
2
3
1.60
EUKARYOTIC DECODING REGION A-SITE RNA
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
26
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
26
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
25
A
N1
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
25
A
O6
G
25
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
25
A
N2
G
25
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
24
A
N3
C
24
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
24
A
O2
C
24
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
24
A
N4
C
24
1_555
hydrog
TYPE_16_PAIR
A
U
5
A
N3
U
5
1_555
A
U
23
A
O4
U
23
1_555
hydrog
TYPE_16_PAIR
A
U
5
A
O2
U
5
1_555
A
U
23
A
N3
U
23
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
A
G
22
A
O6
G
22
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
A
G
22
A
N2
G
22
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
19
A
N2
G
19
1_555
hydrog
C-A MISPAIR
A
C
8
A
O2
C
8
1_555
A
A
20
A
N6
A
20
1_555
hydrog
A-G MISPAIR
A
A
9
A
N6
A
9
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
A
9
A
N1
A
9
1_555
A
U
18
A
N3
U
18
1_555
hydrog
WATSON-CRICK
A
A
9
A
N6
A
9
1_555
A
U
18
A
O4
U
18
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
A
G
17
A
N2
G
17
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
11
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
11
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
11
1_555
A
G
16
A
N2
G
16
1_555
hydrog
U-G MISPAIR
A
U
12
A
O2
U
12
1_555
A
G
15
A
N1
G
15
1_555
RNA
stem-internal loop-stem-tetraloop RNA, G-A base pair, bulged A, RNA
1FYO
PDB
1
1FYO
1
27
1FYO
1
27
1FYO
A
1
1
27
1
P 1