Table S1. Structural parameters of 152 protein-RNA complexes (classified into four different
class based on the type of RNA associated with the protein).
Column headers:
1:
Reference (references are unavailable for two PDB ids 1ZBH and 3QJJ).
2:
PDB id of the protein-RNA complex
3-4:
Protein and RNA components of the complex with length of the protein chain and the RNA
chain are in parentheses.
5.
Resolution of the X-ray structure.
6-7:
Chain ids in the PDB entry. Symmetry-related chains are primed (e.g. A' in 1J1U).
8-10: Total buried surface area (B), area of the protein surface and RNA surface buried in the
complex.
11-12: Number of interface amino acid residues and interface nucleotides.
13-14: f_np: percent fraction of the B contributed by non-polar (carbon containing) groups on the
protein and the RNA side of the interface.
15-16: f_bu: percent fraction of the interface protein and the RNA atoms that are buried (zero
SASA) in the complex.
17-18: LD: packing density index as defined by equation 5 in the text.
19:
N_hb: number of H-bonds between aminoacids and nucleotides at the protein-RNA
interface.
20:
SB: number of salt bridges at protein-RNA interface.
21:
Sc: shape complementarity index of the protein-RNA complex.
22:
GV: mean gap volume index of the protein-RNA complex.
1
Ref.
PDB
id
Composition
Pro
Res
(Å)
RNA
B (Å2)
Chain id
Pro
RNA
2.9
A
R
2.6
P
2.4
Tot
Interface
residues/nt
Pro
RNA
f_np
Pro
f_bu
RNA
Pro
LD
RNA
Pro
N_
hb
SB
Sc
GV
(Å)
Pro
RNA
RNA
4432
2130
2302
82
31
55
28
32
28
48
47
25
6
0.58
8
R
2617
1235
1382
53
18
56
33
23
24
38
39
19
6
0.58
10
A
B
4504
2178
2326
73
32
53
34
33
35
45
48
44
13
0.74
9
2.2
A
B
5769
2663
3106
98
40
59
38
28
20
45
44
41
11
0.67
7
2.2
A
T
4971
2463
2508
80
37
51
34
24
22
42
43
32
13
0.62
3
2.9
A
C
5173
2502
2671
100
41
55
34
24
24
35
40
28
11
0.60
1
2.9
AA'
B
3759
1797
1962
68
29
54
27
19
20
38
36
26
15
0.67
2
2.9
AB
T
2481
1155
1325
39
18
63
31
30
24
41
47
17
6
0.71
20
tRNA-Tyr
(77)
2.0
AA'
B
2242
1065
1177
41
18
51
35
23
23
32
31
19
3
0.75
16
tRNA-Glu
(75)
2.1
A
C
4511
2120
2390
86
32
59
34
27
26
41
44
34
13
0.65
6
tRNA-Thr
(76)
2.9
A
B
4603
2268
2335
78
28
56
35
25
26
38
46
29
8
0.62
9
tRNA-Gln
(75)
2.3
A
B
5203
2427
2775
85
35
53
32
25
25
40
52
38
21
0.67
6
2.9
AB
T
2292
1142
1150
40
18
48
31
17
19
25
28
13
10
0.67
20
2.3
B
A
4558
2152
2406
85
32
54
37
27
29
43
45
28
10
0.60
6
A. tRNA (31)
[1]
1ASY
[2]
1B23
[3]
1C0A
[4]
1F7U
[5]
1FFY
[6]
1GAX
[7]
1H3E
[8]
1H4S
[9]
1J1U
[10]
1N78
[11]
1QF6
[12]
1QTQ
[13]
[14]
1SER
1U0B
Yeast aspartyltRNA
synthetase (490)
T. Aquaticus
EF-TU (405)
E. coli aspartyltRNA
synthetase (585)
Arginyl-tRNA
synthetase (607)
Isoleucyl-tRNA
synthetase (917)
Valyl-tRNA
synthetase (862)
T. thermophilus
tyrosyl-tRNA
synthetase (432)
T. thermophilus
prolyl-tRNA
synthetase
(477+477)
M. jannaschii
Tyrosyl-tRNA
synthetase
(306+306)
T. thermophilus
glutamyl-tRNA
synthetase (468)
E. coli threonyltRNA
synthetase (642)
E. Coli
GlutaminyltRNA
synthetase (553)
T.
thermophilusser
yl-tRNA
synthetase
(421+421)
E.coli cysteinyltRNA
tRNA-Asp
(75)
E. coli
tRNA-Cys
(74)
tRNA-Asp
(77)
tRNA-Arg
(76)
tRNA-Ile
(75)
tRNA-Val
(75)
tRNA-Tyr
(86)
tRNA-Pro
(77)
tRNA-Ser
(94)
tRNA-Cys
(74)
2
[15]
1VFG
[16]
2AZX
[17]
2CSX
[18]
2DLC
[19]
2DRB
[20]
2DU3
[21]
2FK6
[22]
2FMT
synthetase (461)
CCA-adding
enzyme (390)
H. sapiens
tryptophanyltRNA
synthetase (477)
MethionyltRNA
synthetase (497)
Tyrosyl-tRNA
synthetase(394)
CCA-adding
enzyme (437)
OphosphoseryltRNA
synthetase(534+
534+534+534)
RNase Z (320)
MethionyltRNAfmet
transformylase
(314)
Isopentenyltrans
ferase (316)
Arginyl-tRNA
synthetase (629)
[23]
2ZM5
[24]
2ZUE
[25]
2ZZM
[26]
3ADB
[27]
3AMT
[28]
3EPH
[29]
3HL2
Trm5 (336)
OphosphoseryltRNA kinase
(259)
Agmatinylcytidi
ne synthetase
TiaS (440)
DMATase
(409)
Selenium
transferase
(501)
[30]
[31]
3VJR
3ZJT
Peptidyl-tRNA
hydrolase (197)
E.coli leucyl-
tRNA (75)
2.8
B
D
1665
833
832
39
15
48
35
11
10
22
30
11
4
0.66
16
tRNA-Trp
(75)
2.8
AA'
C
2134
1023
1111
40
18
55
27
26
23
32
35
19
4
0.67
20
2.7
A
C
2183
1041
1142
42
22
47
37
32
33
40
43
18
3
0.69
16
2.4
XX'
YY'
4266
2056
2210
72
30
55
36
25
28
34
36
30
4
0.70
13
2.8
A
B
3198
1449
1749
60
18
52
34
35
36
40
48
30
14
0.70
8
2.6
AA'
BB'
DD'
2812
1296
1516
58
30
61
26
24
19
34
32
12
4
0.78
9
2.9
A
R
1531
751
781
23
17
61
39
20
20
27
29
5
8
0.68
14
2.8
A
C
2941
1499
1442
43
25
55
33
20
23
35
46
27
9
0.68
8
2.6
A
C
3937
1953
1983
61
20
56
34
23
29
51
71
32
20
0.64
6
2.0
A
B
4934
2366
2568
85
38
58
34
30
21
41
41
27
10
0.64
9
2.7
A
B
4524
2138
2386
77
30
57
33
25
28
48
51
37
21
0.66
6
2.8
A
C
3099
1579
1521
51
28
57
30
10
14
28
37
14
15
0.57
10
2.9
A
B
3822
1826
1996
66
26
48
31
32
26
50
49
27
14
0.68
8
3.0
A
E
4815
2298
2517
80
27
51
31
30
34
52
69
38
24
0.65
6
2.8
AA'
BB'
E
2186
1092
1094
38
20
50
35
16
18
27
28
15
10
0.61
9
2.4
2.2
A
A
B
B
1355
4323
690
2125
664
2197
21
77
15
35
59
57
32
35
15
14
23
19
25
30
33
32
9
18
4
16
0.61
0.58
9
12
tRNA-Met
(75)
tRNA-Tyr
(76)
tRNAmini
CCA (35)
tRNA-Cys
(71+71)
tRNA-Thr
(79)
tRNAfmet
(77)
tRNA-Phe
(76)
tRNA-Arg
(78)
tRNA-Leu
(84)
tRNA-Sec
(92)
tRNA-Ile
(78)
tRNA-Cys
(69)
tRNA-Sec
(90)
tRNA
CCAacceptor
(36)
tRNA-Leu
3
tRNA
synthetase (880)
(88)
Ribosomal
protein L25 (94)
Ribosomal
protein L5 (206)
Ribosomal
proteins S15,
S6, S18
(98+88+88)
M. jannaschii
ribosomal
protein S8 (130)
T. thermophilus
ribosomal
protein L5 (182)
T. maritima
ribosomal
protein L11
(140)
S.
acidocaldarius
ribosomal
protein L1P
(217)
E. coli
ribosomal
protein S8 (129)
50S ribosomal
protein L7Ae
(117)
Ribosomal
protein L1 (228)
5s rRNA
(19+19)
5s rRNA
(19+21)
dsRBD A
(69+69)
dsRNA
(10+10)
4.5S RNA
domain IV
(49)
RNA
transcript
(10)
B. Ribosomal (10)
[32]
1DFU
[33]
1FEU
[34]
1G1X
[35]
1I6U
[36]
1MJI
[37]
1MMS
[38]
1MZP
[39]
1S03
[40]
1SDS
[41] 2HW8
C. Duplex (49)
[42]
1DI2
[43]
1HQ1
[44]
1MSW
[45]
1N35
[46]
1OOA
E.coli SRP
(105)
T7 RNA
polymerase
(883)
Reovirus
polymerase
(1267)
NF-kappaB p50
(326)
1.8
P
MN
1688
828
860
26
19
47
21
29
32
42
41
17
14
0.67
5
2.3
A
BC
1595
790
806
26
18
40
28
37
41
37
36
24
12
0.71
9
2.6
ABC
DE
4945
2427
2518
73
47
57
28
35
32
43
44
36
22
0.65
5
2.6
A
C
1802
885
916
30
19
55
39
33
25
40
40
16
5
0.56
6
2.5
A
C
1745
878
867
30
17
49
39
24
28
35
38
6
2
0.53
7
2.6
A
C
2455
1200
1255
37
23
52
31
37
39
40
44
24
14
0.73
5
2.7
A
B
2949
1511
1437
39
27
49
27
33
39
40
51
32
23
0.69
5
RNA (47)
box
H/ACA
sRNA (15)
2.7
H
A
1744
848
896
29
16
61
36
24
20
40
41
11
3
0.62
8
1.8
C
FF'
1200
553
647
21
8
56
25
32
27
32
43
15
6
0.74
6
mRNA (36)
2.1
A
B
2401
1164
1237
36
21
69
31
48
48
49
48
19
3
0.64
6
1.9
AB
DE
1840
933
907
30
16
53
30
18
18
25
30
16
5
0.72
4
1.5
A
B
1365
688
676
20
13
54
35
44
47
39
43
15
4
0.77
8
2.1
D
R
1828
902
926
40
10
55
38
11
17
22
33
7
2
0.63
25
2.5
A
BC
3245
1558
1686
72
13
59
30
31
27
41
55
14
4
0.53
17
2.5
A
C
1910
997
913
29
19
51
19
23
20
37
43
17
4
0.60
9
16S rRNA
(41+44)
16S rRNA
(37)
5S rRNA
fragment
(34)
T. maritima
23S rRNA
fragment
(58)
23S rRNA
fragment
(55)
dsRNA
(5+10)
aptamer
RNA (29)
4
[47]
1Q2R
[48]
1R3E
[49]
1R9F
[50]
1SI3
[51]
1WNE
[52]
1YVP
[53]
1ZBI
[54]
2AZ0
[55]
2BGG
[56]
2EZ6
[57]
2F8S
[58]
2GJW
[59]
2GXB
[60]
2OZB
[61]
2PJP
[62]
2QUX
Guanine
transglycosylase
(386+386)
Pseudouridine
Synthase TruB
(309)
p19 (136+136)
PAZ domain of
eIF2c1 (149)
Foot-and-mouth
disease virus
polymerase
(476)
Ro autoantigen
(538)
RNase H
(142+142)
Flock house
virus B2
(73+73)
A. fulgidus
PIWI (427)
RNase III
(221+221)
A. aeolicus
Argonaute
(706+706)
Splicing
endonuclease
(313+313)
Z alpha domain
of adenosine
deaminase (66)
Ribonucleoprot
ein (130+260)
E.coli SelB
(121)
Pseudomonas
phage PP7 coat
protein
(125+125)
20-mer
tRNA
fragment
(20)
tRNA
fragment (
17)
siRNA
(21+21)
siRNA (9)
templateprimer
RNA
decanucleot
ide (8+5)
Y RNA
(10+10+10)
A form
RNA
(12+12)
siRNA
(18+18)
siRNA
(8+8)
28-mer
RNA
(28+28)
siRNA
(22+22)
bulgehelix-bulge
RNA
(19+12+7)
dsRNA
(7+7)
U4snRNA
(33)
SECIS
RNA (23
mer)
hairpin
RNA (25)
2.9
AB
E
3007
1417
1590
52
16
43
36
34
31
41
55
29
7
0.64
8
2.1
A
C
3683
1716
1968
60
23
52
29
36
34
56
64
30
15
0.63
3
1.9
AA'
BC
3217
1535
1682
56
25
62
43
25
22
35
38
20
15
0.66
5
2.6
A
B
1594
765
828
28
9
46
31
28
23
38
40
15
10
0.68
4
3.0
A
BC
3079
1427
1652
58
13
53
33
37
38
42
61
17
6
0.62
6
2.2
B
EFH
4208
1987
2221
75
21
54
30
30
35
48
47
39
6
0.68
6
1.9
A
CD
1675
790
885
29
12
41
30
34
47
42
49
15
2
0.69
3
2.6
AB
CD
2264
1103
1161
30
18
57
36
30
33
38
38
22
8
0.69
4
2.2
A
PQ
2241
1027
1214
36
11
51
34
37
33
41
55
20
9
0.73
7
2.1
AB
CD
5194
2617
2577
83
44
55
36
25
26
34
41
45
10
0.66
6
3.0
AB
CD
990
488
502
20
6
52
40
18
16
28
43
2
2
0.74
33
2.9
AB
EFH
3244
1525
1718
57
19
56
40
39
31
52
51
14
12
0.62
10
2.3
A
EF
769
363
406
12
7
62
24
29
30
35
32
5
3
0.76
5
2.6
AB
C
2569
1261
1308
42
17
58
28
26
33
37
61
24
12
0.61
8
2.3
A
B
1300
628
673
21
8
40
26
31
31
34
29
16
11
0.76
5
2.4
AB
C
1754
801
953
35
11
38
29
22
29
28
35
26
5
0.77
8
5
synthetic FAB
(214+224)
[63]
2R8S
[64]
2XD0
[65]
2Y8W
P. atrosepticum
ToxN (171)
Endoribonuclea
se Cse3 (215)
[66]
2YKG
RIG-I (696)
[67]
2ZI0
[68]
2ZKO
TAV2b (75+75)
NS1 protein of
influenza A
(73+73)
[69]
3A6P
[70]
3BSN
Exp-5:RanGTP
(1024+13+216)
Norwalk virus
polymerase
(510)
[71]
3BT7
Methyltransfera
se TrmA (369)
[72]
3DD2
Thrombin (258)
[73]
3DH3
[74]
3EQT
[75]
3FTE
RluF (290)
Helicase
DHX58 (145)
Methyltransfera
se KsgA (249)
[76]
3IAB
[77]
3KS8
[78]
3MOJ
[79]
3O3I
[80]
[81]
3OIJ
3OL6
RNases P/MRP
(158+140)
Polymerase
cofactor VP35
(184+184)
Helicase dbpA
(76)
Hiwi1 PAZ
domain (124)
Methyltransfera
se (253+253)
Poliovirus
ribozyme
(159)
P.
atrosepticu
m ToxI (36)
hairpin
RNA (20)
dsRNA
(10+10)
siRNA
(21+21)
A-form
dsRNA
(21+21)
premicroRNA
(24+24)
2.0
LH
R
2510
1194
1316
42
27
53
33
29
22
48
40
25
2
0.71
22
3.0
A
G
1887
882
1005
35
15
59
28
29
24
39
36
8
3
0.53
6
1.8
A
B
3258
1528
1730
50
17
46
28
30
27
51
51
44
20
0.72
3
2.5
A
CD
2150
985
1165
45
16
70
35
22
24
31
39
13
3
0.68
19
2.8
AB
CD
4574
2341
2234
54
39
44
17
18
23
39
43
41
43
0.70
3
1.7
AB
CD
2466
1238
1228
34
20
65
36
16
31
40
47
16
18
0.62
6
2.9
ABC
DE
4223
2043
2180
77
34
52
37
19
19
35
39
14
18
0.53
17
RNA (8+9)
T-arm
analogue
(19)
26-mer
RNA (26)
23S RNA
(22)
1.8
A
PT
3112
1448
1663
71
17
59
27
20
22
38
43
22
9
0.61
7
2.4
A
C
2230
982
1249
42
12
48
33
32
32
47
53
30
7
0.58
8
1.9
H
B
1823
892
931
26
15
44
28
20
25
35
48
17
7
0.70
7
3.0
B
F
3425
1664
1761
56
18
42
27
38
45
60
71
44
19
0.67
4
dsRNA (8)
rRNA
(22+22)
RNase
MRP P3
domain
(46)
2.0
AB
CD
2706
1216
1490
48
16
66
35
33
40
38
52
24
8
0.69
5
3.0
A
CD
837
429
407
17
13
63
37
7
9
15
24
2
3
0.46
24
2.7
AB
R
5088
2387
2701
81
29
62
32
34
32
55
60
35
11
0.70
3
2.4
AB
EF
1664
799
864
32
12
54
35
19
26
34
46
11
10
0.59
9
2.9
B
A
1759
857
902
27
15
58
31
32
22
38
40
13
8
0.70
8
2.8
X
A
923
405
518
20
5
50
30
45
40
41
37
14
0
0.71
6
3.0
2.5
AB
A
C
BCD
2070
4175
999
1999
1072
2176
35
79
10
22
50
59
37
32
39
24
48
26
47
42
63
52
22
23
7
12
0.77
0.56
10
6
dsRNA
(18+18)
E.coli 23S
rRNA
fragment
(74)
piRNA (14)
SSU rRNA
(14+14)
RNA
6
[82]
3RW6
[83]
3SNP
[84]
3ZC0
[85]
4ATO
[86]
4ERD
polymerase
(471)
Nuclear RNA
export factor 1
(267)
Iron regulatory
protein 1 (908)
A. fulgidus
C3PO
(199+199+199+
199+199+199+
199+199)
B. thuringiensis
ToxN
(194+194+194)
p65 C-terminal
domain
(129+129)
Exonuclease
[87] 4FVU
(243)
Oligoadenylate
synthetase 1
[88] 4IG8
(349)
Endoribonuclea
se Cas6
[89] 4ILL
(289+289)
Bacteriophage
Qβ coat protein
[90] 4L8H
(132+132)
D. Single-stranded (62)
Cap-specific
mRNA
methyltransfera
[91] 1AV6
se (295)
[92] 1C9S
TRAP (74)
poly(A)-binding
[93] 1CVJ
protein (190)
RRMdomain of
the HuD protein
(167)
[94] 1G2E
Restrictocin
(149)
[95] 1JBS
H. sapiens
[96] 1JID
SRP19 (128)
(26+14+9)
CTE RNA
(62)
ferritin H
IRE RNA
(30)
duplex
RNA
(16+16)
B.
thuringiensi
s ToxI (34)
stem IV of
telomerase
RNA
(22+22)
dsRNA
(8+8)
dsRNA
(18+18)
CRISPR
RNA
(24+24)
operator
hairpin
RNA (20)
M7G
capped
RNA (6)
ssRNA (7)
polyA (11)
class II
ARE
fragment
(10)
SRD RNA
Analogue
(29 mer)
SRP RNA
(29)
2.3
A
H
2699
1319
1380
44
28
54
38
23
25
39
38
10
3
0.61
8
2.8
A
C
2872
1351
1522
60
18
50
34
28
30
38
45
23
6
0.63
13
3.0
AA'
BB'C
C'D
D'
MM'
2324
1123
1201
48
18
37
21
3
15
28
40
14
22
0.64
39
2.2
A
G
2265
1104
1161
33
12
51
30
23
32
45
49
26
10
0.74
5
2.6
AB
CD
3281
1590
1690
47
18
66
38
26
44
39
48
20
13
0.69
6
2.9
A
BC
1240
575
666
24
9
42
34
30
35
37
44
10
2
0.59
8
2.7
A
BC
2914
1416
1499
48
20
50
35
26
25
41
43
26
10
0.58
7
2.5
AB
RC
7076
3272
3804
115
33
53
32
34
34
50
62
53
28
0.66
4
2.4
AB
R
1995
914
1081
33
12
43
32
22
20
36
37
17
11
0.66
6
2.8
1.9
A
L
B
W1-7
845
1028
385
487
460
541
19
18
4
6
60
58
32
33
22
39
28
29
30
40
38
39
5
8
3
0
0.61
0.79
14
3
2.6
A
M
2823
1196
1626
48
9
51
39
44
33
56
53
24
4
0.73
2
2.3
A
B
2776
1322
1454
45
10
55
35
33
34
49
59
17
8
0.69
3
2.0
A
C
1313
668
645
28
14
51
35
14
20
25
37
8
7
0.70
7
1.8
A
B
1436
703
733
26
10
48
23
27
20
29
38
17
19
0.76
6
7
[97]
1K8W
[98]
1KNZ
[99]
1KQ2
[100]
1LNG
[101]
1M5O
[102]
1M8V
[103]
1M8W
[104]
1UVI
[105]
1WPU
[106]
1WSU
NA
1ZBH
[107]
1ZH5
[108]
2A8V
[109]
[110]
2ANR
2ASB
[111]
2B3J
[112]
[113]
2BH2
2BX2
[114]
2DB3
Pseudouridine
synthase B
(327)
Rotavirus NSP3
(164)
Hfq
(77+77+77+77+
77+77)
M. jannaschii
SRP19 (87)
U1 Snp (100)
P. abyssi Sm
PROTEIN
(77+77)
Pumiliohomology
domain (349)
phi6 RNA
polymerase
(664)
HutP
antitermination
protein (147)
Elongation
Factor SelB
(124)
exonuclease
ERI1
(299+299)
La autoantigen
(195+195)
RHO (118)
Nova-1
KH1/KH2
domain (178)
Nus A (251)
TadA (159)
Methyltransfera
se RumA (433)
RNase E (517)
DEAD-box
helicase vasa
T stemloop RNA
(22)
1.9
A
B
2974
1342
1632
49
13
56
28
44
45
57
75
26
9
0.65
4
mRNA (5)
2.5
AB
W
1921
762
1159
40
5
50
36
47
54
59
61
30
7
0.74
5
2.7
ABH
IKM
R
3026
1354
1672
44
7
73
38
48
46
60
70
14
0
0.60
5
2.3
A
B
2368
1145
1223
30
22
56
22
33
31
40
44
29
18
0.67
9
2.2
C
B
1767
822
944
29
13
52
30
34
29
46
43
18
3
0.79
10
2.6
AM
O
1289
603
687
22
6
65
40
28
26
30
53
6
2
0.74
4
Nre1-19
RNA (8+8)
2.2
A
CE
2142
973
1169
38
14
45
39
35
45
37
70
27
1
0.71
5
6-mer RNA
(6)
2.2
A
D
1814
780
1034
46
4
53
41
41
43
49
49
7
2
0.59
14
1.5
A
C
1358
623
735
27
7
73
45
47
35
48
46
9
0
0.71
4
2.3
A
E
938
452
486
13
6
51
23
26
32
28
34
11
8
0.71
8
3.0
AD
E
1756
886
870
27
12
54
30
16
19
31
43
7
7
0.67
16
1.9
AB
C
1849
830
1020
32
9
65
38
27
25
33
37
8
1
0.69
13
2.4
B
E
719
281
438
17
4
78
35
45
33
41
33
6
0
0.79
7
1.9
1.5
A
A
B
B
1220
2317
583
1092
636
1225
21
40
10
11
66
69
33
43
40
46
32
37
34
44
50
53
10
17
3
1
0.70
0.75
7
4
2.0
AB
E
2099
1007
1092
40
10
53
43
39
47
50
67
20
9
0.62
5
2.2
2.9
A
L
C
R
4492
912
2153
419
2339
493
78
22
25
4
48
57
32
32
30
27
32
20
49
35
57
37
40
4
16
4
0.70
0.66
4
29
2.2
A
E
1193
494
699
26
6
56
19
43
37
37
44
20
6
0.73
16
7-mer RNA
(7)
7S SRP
RNA (97)
Hairpin
ribozyme
(92)
Uridine
Heptamer
(7)
hut mRNA
(7)
SECIS
RNA (23
mer)
Histone
mRNA (20
mer)
3'-terminii
mRNA (9)
Cytosine
rich RNA
(6)
hairpin
RNA (25)
rRNA (11)
tRNA-Arg2
(16)
23S rRNA
(37)
RNA (15)
ssRNA (10)
8
(434)
Splicing factor
U2AF (172)
VSV
nucleocapsid
(422)
Pseudouridine
synthase RluA
(217)
RNase II (664)
Exon junction
complex
(410+146+89+1
50)
S. solfataricus
exosome
(277+250)
Serine protease
subunit NS3
(451)
Poly(rC)binding protein
2 (73)
S.cerevisiae
poly(A)
polymerase
(525)
Rotavirus
polymerase
VP1 (1095)
Exonuclease
Rrp44 (760)
Mtr4 (1010)
[115]
2G4B
[116]
2GIC
[117]
[118]
2I82
2IX1
[119]
2J0S
[120]
2JEA
[121]
2JLU
[122]
2PY9
[123]
2Q66
[124]
2R7R
[125]
[126]
2VNU
2XGJ
[127]
2XNR
[128]
2XS2
[129]
2XZO
Nab3-RRM
(97)
Murine Dazl
(102)
Upf1 helicase
(623)
[130]
3AEV
Dim2p (219)
[131]
3BX2
PUF4 (335)
Polypyrimi
dine (7)
viral
genomic
RNA (45)
2.5
A
B
1162
543
619
20
5
54
39
32
22
45
43
6
1
0.69
5
2.9
A
R
1999
985
1014
36
11
55
36
16
19
32
49
10
11
0.57
3
tRNA-Phe
(21)
polyA (13)
2.1
2.7
A
A
E
B
3019
4161
1453
1935
1565
2227
44
82
14
13
53
61
35
40
33
23
36
32
56
42
68
60
29
20
15
5
0.62
0.69
3
8
mRNA (15)
2.2
ACD
T
E
1436
591
845
30
6
61
25
46
38
38
46
21
9
0.75
19
substrate
RNA (35)
2.3
AB
C
1533
693
840
30
5
53
37
19
24
34
42
7
7
0.56
13
ssRNA (12)
human
telomeric
RNA (12)
2.0
A
C
1926
846
1079
40
7
61
34
29
35
41
50
19
9
0.68
11
2.6
B
E
1061
513
548
19
7
55
33
34
39
37
41
9
0
0.72
3
polyA (5)
1.8
A
X
1811
815
996
39
4
64
39
19
21
45
49
12
1
0.68
12
RNA (7)
2.6
A
X
1955
906
1049
41
7
62
34
20
25
35
51
16
3
0.60
28
ssRNA (10)
polyA (5)
UCUU
recognition
sequence
(12)
3'-UTRs of
mRNA (8)
2.3
2.9
D
A
B
C
3166
1389
1454
641
1712
748
66
30
10
5
53
62
37
30
33
25
37
23
44
34
62
49
22
10
9
0
0.69
0.68
10
31
1.6
A
C
926
404
522
16
5
70
39
38
24
41
37
8
1
0.79
2
1.4
A
B
1298
606
692
23
6
57
35
33
25
45
50
9
3
0.76
3
polyU (7)
P.
horikoshii
16S rRNA
fragment
(11)
3' UTR
binding
2.4
A
D
2006
937
1069
43
7
66
27
32
37
39
56
20
0
0.70
14
2.8
B
C
2416
1132
1285
40
11
62
36
35
31
42
45
21
4
0.70
3
2.8
A
C
2467
1098
1370
43
9
46
41
40
39
38
44
19
1
0.68
4
9
[132]
[133]
3D2S
3I5X
[134]
[135]
3IEV
3K5Q
[136]
3MDG
[137]
3NMR
[138]
[139]
3O8C
3PF4
NA
3QJJ
[140]
3R2C
[141]
3RC8
[142]
3T5N
[143]
4E78
[144]
[145]
4H5P
4HOR
[146]
[147]
4J1G
4J7M
[148]
4M59
[149]
4MDX
[150]
4N2Q
MBNL1 ZnF3/4
(70)
Mss116p (563)
GTPase era
(308)
FBF (412)
CFI(m)25
(227+227)
CUG-binding
protein 1 (175)
HCV NS3
helicase (666)
CspB (67+67)
RAMP Protein
(243)
NusB-NusE
(148+83)
Helicase
SUPV3L1 (677)
Lassa virus
nucleoprotein
(354)
HCV
polymerase
(572)
Nucleocapsid
(245+245)
IFIT (482)
Nucleocapsid
(235+235+235+
235)
Dom3Z (378)
Chloroplast
ppr10
(718+718)
mRNA
interferase
MazF
(117+117)
Thylakoid
assembly 8
(258)
sequence
(9)
pre-mRNA
(6)
polyU (10)
16S rRNA
(12)
mRNA (9)
pre-mRNA
(6)
UGU-rich
mRNA (12)
1.7
1.9
A
A
E
B
569
2228
273
969
296
1259
12
44
3
10
34
62
32
33
27
44
21
32
26
42
28
43
7
24
1
9
0.81
0.72
7
10
1.9
2.2
A
A
D
B
2273
2597
1014
1177
1260
1420
38
40
9
9
65
52
39
40
47
32
38
32
51
41
51
46
19
21
2
2
0.77
0.62
5
5
2.2
AB
C
1069
503
566
23
6
66
40
27
38
37
48
6
0
0.76
17
1.9
A
B
1097
489
608
21
6
66
33
32
30
36
36
5
2
0.83
5
polyU (6)
ssRNA (7)
CRISPR
Repeat
RNA (12)
BoxA RNA
(12)
RNA
fragment
(6)
2.0
1.4
A
B
C
R
1909
893
909
419
1000
474
36
16
6
5
54
72
33
40
29
40
34
28
41
42
56
37
13
4
8
0
0.74
0.81
14
3
2.8
A
Q
3191
1490
1701
52
12
53
32
44
40
50
63
27
9
0.65
3
1.9
AJ
R
2273
1029
1243
37
9
62
35
50
35
54
54
23
1
0.78
4
2.9
A
E
1471
668
802
32
6
65
31
34
31
37
49
10
1
0.63
19
ssRNA (6)
RNA
primertemplate
pair (6+6)
1.8
A
C
1910
857
1053
38
6
50
35
38
33
51
59
22
6
0.68
6
2.9
A
PT
2100
1006
1095
46
10
53
38
17
26
34
50
13
7
0.51
9
polyU (14)
polyC (5)
2.2
1.9
AB
A
E
X
4483
1748
2173
765
2310
983
76
45
14
4
65
46
29
22
26
28
31
31
52
50
68
53
21
14
24
6
0.67
0.59
4
11
polyU (45)
polyU (5)
2.8
1.7
C
A
E1934
B
3039
1268
1488
589
1550
679
47
29
14
5
60
46
33
26
19
24
33
27
42
40
60
42
13
9
12
8
0.56
0.60
1
13
psaJ RNA
(18+18)
2.5
AB
CD
7843
3665
4178
157
31
64
36
32
33
39
54
31
19
0.60
9
1.5
AB
C
2127
958
1169
41
8
64
37
42
40
48
47
19
2
0.75
4
2.8
A
B
814
375
439
10
5
60
28
31
33
40
39
4
6
0.70
10
mRNA (9)
Zm4 13mer RNA
(13)
10
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
Ruff, M., et al., Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science,
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Nissen, P., et al., The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.
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Eiler, S., et al., Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step. EMBO J, 1999. 18(22): p. 6532-41.
Delagoutte, B., D. Moras, and J. Cavarelli, tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding. EMBO
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Silvian, L.F., J. Wang, and T.A. Steitz, Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science, 1999.
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Yaremchuk, A., et al., Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J, 2002. 21(14): p. 3829-40.
Yaremchuk, A., et al., A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyltRNA synthetase: comparison with histidyl-tRNA synthetase. J Mol Biol, 2001. 309(4): p. 989-1002.
Kobayashi, T., et al., Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol, 2003.
10(6): p. 425-32.
Sekine, S., et al., ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J, 2003. 22(3): p. 676-88.
Sankaranarayanan, R., et al., The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential
zinc ion in the active site. Cell, 1999. 97(3): p. 371-81.
Rath, V.L., et al., How glutaminyl-tRNA synthetase selects glutamine. Structure, 1998. 6(4): p. 439-49.
Biou, V., et al., The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science, 1994. 263(5152): p. 1404-10.
Hauenstein, S., et al., Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol, 2004. 11(11): p. 1134-41.
Tomita, K., et al., Structural basis for template-independent RNA polymerization. Nature, 2004. 430(7000): p. 700-4.
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