Table S1. Structural Parameters of 152 Protein-RNA Complexes (Classified Into Four Different

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 / Res
(Å) / Chain id / B (Å2) / Interface residues/nt / f_np / f_bu / LD / N_ hb / SB / Sc / GV (Å)
Pro / RNA / Pro / RNA / Tot / Pro / RNA / Pro / RNA / Pro / RNA / Pro / RNA / Pro / RNA
A. tRNA (31)
[1] / 1ASY / Yeast aspartyl-tRNA synthetase (490) / tRNA-Asp (75) / 2.9 / A / R / 4432 / 2130 / 2302 / 82 / 31 / 55 / 28 / 32 / 28 / 48 / 47 / 25 / 6 / 0.58 / 8
[2] / 1B23 / T. Aquaticus EF-TU (405) / E. coli tRNA-Cys (74) / 2.6 / P / R / 2617 / 1235 / 1382 / 53 / 18 / 56 / 33 / 23 / 24 / 38 / 39 / 19 / 6 / 0.58 / 10
[3] / 1C0A / E. coli aspartyl-tRNA synthetase (585) / tRNA-Asp (77) / 2.4 / A / B / 4504 / 2178 / 2326 / 73 / 32 / 53 / 34 / 33 / 35 / 45 / 48 / 44 / 13 / 0.74 / 9
[4] / 1F7U / Arginyl-tRNA synthetase (607) / tRNA-Arg (76) / 2.2 / A / B / 5769 / 2663 / 3106 / 98 / 40 / 59 / 38 / 28 / 20 / 45 / 44 / 41 / 11 / 0.67 / 7
[5] / 1FFY / Isoleucyl-tRNA synthetase (917) / tRNA-Ile (75) / 2.2 / A / T / 4971 / 2463 / 2508 / 80 / 37 / 51 / 34 / 24 / 22 / 42 / 43 / 32 / 13 / 0.62 / 3
[6] / 1GAX / Valyl-tRNA synthetase (862) / tRNA-Val (75) / 2.9 / A / C / 5173 / 2502 / 2671 / 100 / 41 / 55 / 34 / 24 / 24 / 35 / 40 / 28 / 11 / 0.60 / 1
[7] / 1H3E / T. thermophilus tyrosyl-tRNA synthetase (432) / tRNA-Tyr (86) / 2.9 / AA' / B / 3759 / 1797 / 1962 / 68 / 29 / 54 / 27 / 19 / 20 / 38 / 36 / 26 / 15 / 0.67 / 2
[8] / 1H4S / T. thermophilus prolyl-tRNA synthetase (477+477) / tRNA-Pro (77) / 2.9 / AB / T / 2481 / 1155 / 1325 / 39 / 18 / 63 / 31 / 30 / 24 / 41 / 47 / 17 / 6 / 0.71 / 20
[9] / 1J1U / M. jannaschii Tyrosyl-tRNA synthetase (306+306) / tRNA-Tyr (77) / 2.0 / AA' / B / 2242 / 1065 / 1177 / 41 / 18 / 51 / 35 / 23 / 23 / 32 / 31 / 19 / 3 / 0.75 / 16
[10] / 1N78 / T. thermophilus glutamyl-tRNA synthetase (468) / tRNA-Glu (75) / 2.1 / A / C / 4511 / 2120 / 2390 / 86 / 32 / 59 / 34 / 27 / 26 / 41 / 44 / 34 / 13 / 0.65 / 6
[11] / 1QF6 / E. coli threonyl-tRNA synthetase (642) / tRNA-Thr (76) / 2.9 / A / B / 4603 / 2268 / 2335 / 78 / 28 / 56 / 35 / 25 / 26 / 38 / 46 / 29 / 8 / 0.62 / 9
[12] / 1QTQ / E. Coli Glutaminyl-tRNA synthetase (553) / tRNA-Gln (75) / 2.3 / A / B / 5203 / 2427 / 2775 / 85 / 35 / 53 / 32 / 25 / 25 / 40 / 52 / 38 / 21 / 0.67 / 6
[13] / 1SER / T. thermophilusseryl-tRNA synthetase (421+421) / tRNA-Ser (94) / 2.9 / AB / T / 2292 / 1142 / 1150 / 40 / 18 / 48 / 31 / 17 / 19 / 25 / 28 / 13 / 10 / 0.67 / 20
[14] / 1U0B / E.coli cysteinyl-tRNA synthetase (461) / tRNA-Cys (74) / 2.3 / B / A / 4558 / 2152 / 2406 / 85 / 32 / 54 / 37 / 27 / 29 / 43 / 45 / 28 / 10 / 0.60 / 6
[15] / 1VFG / CCA-adding enzyme (390) / tRNA (75) / 2.8 / B / D / 1665 / 833 / 832 / 39 / 15 / 48 / 35 / 11 / 10 / 22 / 30 / 11 / 4 / 0.66 / 16
[16] / 2AZX / H. sapiens tryptophanyl-tRNA synthetase (477) / tRNA-Trp (75) / 2.8 / AA' / C / 2134 / 1023 / 1111 / 40 / 18 / 55 / 27 / 26 / 23 / 32 / 35 / 19 / 4 / 0.67 / 20
[17] / 2CSX / Methionyl-tRNA synthetase (497) / tRNA-Met (75) / 2.7 / A / C / 2183 / 1041 / 1142 / 42 / 22 / 47 / 37 / 32 / 33 / 40 / 43 / 18 / 3 / 0.69 / 16
[18] / 2DLC / Tyrosyl-tRNA synthetase(394) / tRNA-Tyr (76) / 2.4 / XX' / YY' / 4266 / 2056 / 2210 / 72 / 30 / 55 / 36 / 25 / 28 / 34 / 36 / 30 / 4 / 0.70 / 13
[19] / 2DRB / CCA-adding enzyme (437) / tRNAminiCCA (35) / 2.8 / A / B / 3198 / 1449 / 1749 / 60 / 18 / 52 / 34 / 35 / 36 / 40 / 48 / 30 / 14 / 0.70 / 8
[20] / 2DU3 / O-phosphoseryl-tRNA synthetase(534+534+534+534) / tRNA-Cys (71+71) / 2.6 / AA'BB' / DD' / 2812 / 1296 / 1516 / 58 / 30 / 61 / 26 / 24 / 19 / 34 / 32 / 12 / 4 / 0.78 / 9
[21] / 2FK6 / RNase Z (320) / tRNA-Thr (79) / 2.9 / A / R / 1531 / 751 / 781 / 23 / 17 / 61 / 39 / 20 / 20 / 27 / 29 / 5 / 8 / 0.68 / 14
[22] / 2FMT / Methionyl-tRNAfmet transformylase (314) / tRNAfmet (77) / 2.8 / A / C / 2941 / 1499 / 1442 / 43 / 25 / 55 / 33 / 20 / 23 / 35 / 46 / 27 / 9 / 0.68 / 8
[23] / 2ZM5 / Isopentenyltransferase (316) / tRNA-Phe (76) / 2.6 / A / C / 3937 / 1953 / 1983 / 61 / 20 / 56 / 34 / 23 / 29 / 51 / 71 / 32 / 20 / 0.64 / 6
[24] / 2ZUE / Arginyl-tRNA synthetase (629) / tRNA-Arg (78) / 2.0 / A / B / 4934 / 2366 / 2568 / 85 / 38 / 58 / 34 / 30 / 21 / 41 / 41 / 27 / 10 / 0.64 / 9
[25] / 2ZZM / Trm5 (336) / tRNA-Leu (84) / 2.7 / A / B / 4524 / 2138 / 2386 / 77 / 30 / 57 / 33 / 25 / 28 / 48 / 51 / 37 / 21 / 0.66 / 6
[26] / 3ADB / O-phosphoseryl-tRNA kinase (259) / tRNA-Sec (92) / 2.8 / A / C / 3099 / 1579 / 1521 / 51 / 28 / 57 / 30 / 10 / 14 / 28 / 37 / 14 / 15 / 0.57 / 10
[27] / 3AMT / Agmatinylcytidine synthetase TiaS (440) / tRNA-Ile (78) / 2.9 / A / B / 3822 / 1826 / 1996 / 66 / 26 / 48 / 31 / 32 / 26 / 50 / 49 / 27 / 14 / 0.68 / 8
[28] / 3EPH / DMATase (409) / tRNA-Cys (69) / 3.0 / A / E / 4815 / 2298 / 2517 / 80 / 27 / 51 / 31 / 30 / 34 / 52 / 69 / 38 / 24 / 0.65 / 6
[29] / 3HL2 / Selenium transferase (501) / tRNA-Sec (90) / 2.8 / AA'BB' / E / 2186 / 1092 / 1094 / 38 / 20 / 50 / 35 / 16 / 18 / 27 / 28 / 15 / 10 / 0.61 / 9
[30] / 3VJR / Peptidyl-tRNA hydrolase (197) / tRNA CCA-acceptor (36) / 2.4 / A / B / 1355 / 690 / 664 / 21 / 15 / 59 / 32 / 15 / 23 / 25 / 33 / 9 / 4 / 0.61 / 9
[31] / 3ZJT / E.coli leucyl-tRNA synthetase (880) / tRNA-Leu (88) / 2.2 / A / B / 4323 / 2125 / 2197 / 77 / 35 / 57 / 35 / 14 / 19 / 30 / 32 / 18 / 16 / 0.58 / 12
B. Ribosomal (10)
[32] / 1DFU / Ribosomal protein L25 (94) / 5s rRNA (19+19) / 1.8 / P / MN / 1688 / 828 / 860 / 26 / 19 / 47 / 21 / 29 / 32 / 42 / 41 / 17 / 14 / 0.67 / 5
[33] / 1FEU / Ribosomal protein L5 (206) / 5s rRNA (19+21) / 2.3 / A / BC / 1595 / 790 / 806 / 26 / 18 / 40 / 28 / 37 / 41 / 37 / 36 / 24 / 12 / 0.71 / 9
[34] / 1G1X / Ribosomal proteins S15, S6, S18 (98+88+88) / 16S rRNA (41+44) / 2.6 / ABC / DE / 4945 / 2427 / 2518 / 73 / 47 / 57 / 28 / 35 / 32 / 43 / 44 / 36 / 22 / 0.65 / 5
[35] / 1I6U / M. jannaschii ribosomal protein S8 (130) / 16S rRNA (37) / 2.6 / A / C / 1802 / 885 / 916 / 30 / 19 / 55 / 39 / 33 / 25 / 40 / 40 / 16 / 5 / 0.56 / 6
[36] / 1MJI / T. thermophilus ribosomal protein L5 (182) / 5S rRNA fragment (34) / 2.5 / A / C / 1745 / 878 / 867 / 30 / 17 / 49 / 39 / 24 / 28 / 35 / 38 / 6 / 2 / 0.53 / 7
[37] / 1MMS / T. maritima ribosomal protein L11 (140) / T. maritima 23S rRNA fragment (58) / 2.6 / A / C / 2455 / 1200 / 1255 / 37 / 23 / 52 / 31 / 37 / 39 / 40 / 44 / 24 / 14 / 0.73 / 5
[38] / 1MZP / S. acidocaldarius ribosomal protein L1P (217) / 23S rRNA fragment (55) / 2.7 / A / B / 2949 / 1511 / 1437 / 39 / 27 / 49 / 27 / 33 / 39 / 40 / 51 / 32 / 23 / 0.69 / 5
[39] / 1S03 / E. coli ribosomal protein S8 (129) / RNA (47) / 2.7 / H / A / 1744 / 848 / 896 / 29 / 16 / 61 / 36 / 24 / 20 / 40 / 41 / 11 / 3 / 0.62 / 8
[40] / 1SDS / 50S ribosomal protein L7Ae (117) / box H/ACA sRNA (15) / 1.8 / C / FF' / 1200 / 553 / 647 / 21 / 8 / 56 / 25 / 32 / 27 / 32 / 43 / 15 / 6 / 0.74 / 6
[41] / 2HW8 / Ribosomal protein L1 (228) / mRNA (36) / 2.1 / A / B / 2401 / 1164 / 1237 / 36 / 21 / 69 / 31 / 48 / 48 / 49 / 48 / 19 / 3 / 0.64 / 6
C. Duplex (49)
[42] / 1DI2 / dsRBD A (69+69) / dsRNA (10+10) / 1.9 / AB / DE / 1840 / 933 / 907 / 30 / 16 / 53 / 30 / 18 / 18 / 25 / 30 / 16 / 5 / 0.72 / 4
[43] / 1HQ1 / E.coli SRP (105) / 4.5S RNA domain IV (49) / 1.5 / A / B / 1365 / 688 / 676 / 20 / 13 / 54 / 35 / 44 / 47 / 39 / 43 / 15 / 4 / 0.77 / 8
[44] / 1MSW / T7 RNA polymerase (883) / RNA transcript (10) / 2.1 / D / R / 1828 / 902 / 926 / 40 / 10 / 55 / 38 / 11 / 17 / 22 / 33 / 7 / 2 / 0.63 / 25
[45] / 1N35 / Reovirus polymerase (1267) / dsRNA (5+10) / 2.5 / A / BC / 3245 / 1558 / 1686 / 72 / 13 / 59 / 30 / 31 / 27 / 41 / 55 / 14 / 4 / 0.53 / 17
[46] / 1OOA / NF-kappaB p50 (326) / aptamer RNA (29) / 2.5 / A / C / 1910 / 997 / 913 / 29 / 19 / 51 / 19 / 23 / 20 / 37 / 43 / 17 / 4 / 0.60 / 9
[47] / 1Q2R / Guanine transglycosylase (386+386) / 20-mer tRNA fragment (20) / 2.9 / AB / E / 3007 / 1417 / 1590 / 52 / 16 / 43 / 36 / 34 / 31 / 41 / 55 / 29 / 7 / 0.64 / 8
[48] / 1R3E / Pseudouridine Synthase TruB (309) / tRNA fragment ( 17) / 2.1 / A / C / 3683 / 1716 / 1968 / 60 / 23 / 52 / 29 / 36 / 34 / 56 / 64 / 30 / 15 / 0.63 / 3
[49] / 1R9F / p19 (136+136) / siRNA (21+21) / 1.9 / AA' / BC / 3217 / 1535 / 1682 / 56 / 25 / 62 / 43 / 25 / 22 / 35 / 38 / 20 / 15 / 0.66 / 5
[50] / 1SI3 / PAZ domain of eIF2c1 (149) / siRNA (9) / 2.6 / A / B / 1594 / 765 / 828 / 28 / 9 / 46 / 31 / 28 / 23 / 38 / 40 / 15 / 10 / 0.68 / 4
[51] / 1WNE / Foot-and-mouth disease virus polymerase (476) / template-primer RNA decanucleotide (8+5) / 3.0 / A / BC / 3079 / 1427 / 1652 / 58 / 13 / 53 / 33 / 37 / 38 / 42 / 61 / 17 / 6 / 0.62 / 6
[52] / 1YVP / Ro autoantigen (538) / Y RNA (10+10+10) / 2.2 / B / EFH / 4208 / 1987 / 2221 / 75 / 21 / 54 / 30 / 30 / 35 / 48 / 47 / 39 / 6 / 0.68 / 6
[53] / 1ZBI / RNase H (142+142) / A form RNA (12+12) / 1.9 / A / CD / 1675 / 790 / 885 / 29 / 12 / 41 / 30 / 34 / 47 / 42 / 49 / 15 / 2 / 0.69 / 3
[54] / 2AZ0 / Flock house virus B2 (73+73) / siRNA (18+18) / 2.6 / AB / CD / 2264 / 1103 / 1161 / 30 / 18 / 57 / 36 / 30 / 33 / 38 / 38 / 22 / 8 / 0.69 / 4
[55] / 2BGG / A. fulgidus PIWI (427) / siRNA (8+8) / 2.2 / A / PQ / 2241 / 1027 / 1214 / 36 / 11 / 51 / 34 / 37 / 33 / 41 / 55 / 20 / 9 / 0.73 / 7
[56] / 2EZ6 / RNase III (221+221) / 28-mer RNA (28+28) / 2.1 / AB / CD / 5194 / 2617 / 2577 / 83 / 44 / 55 / 36 / 25 / 26 / 34 / 41 / 45 / 10 / 0.66 / 6
[57] / 2F8S / A. aeolicus Argonaute (706+706) / siRNA (22+22) / 3.0 / AB / CD / 990 / 488 / 502 / 20 / 6 / 52 / 40 / 18 / 16 / 28 / 43 / 2 / 2 / 0.74 / 33
[58] / 2GJW / Splicing endonuclease (313+313) / bulge-helix-bulge RNA (19+12+7) / 2.9 / AB / EFH / 3244 / 1525 / 1718 / 57 / 19 / 56 / 40 / 39 / 31 / 52 / 51 / 14 / 12 / 0.62 / 10
[59] / 2GXB / Z alpha domain of adenosine deaminase (66) / dsRNA (7+7) / 2.3 / A / EF / 769 / 363 / 406 / 12 / 7 / 62 / 24 / 29 / 30 / 35 / 32 / 5 / 3 / 0.76 / 5
[60] / 2OZB / Ribonucleoprotein (130+260) / U4snRNA (33) / 2.6 / AB / C / 2569 / 1261 / 1308 / 42 / 17 / 58 / 28 / 26 / 33 / 37 / 61 / 24 / 12 / 0.61 / 8
[61] / 2PJP / E.coli SelB (121) / SECIS RNA (23 mer) / 2.3 / A / B / 1300 / 628 / 673 / 21 / 8 / 40 / 26 / 31 / 31 / 34 / 29 / 16 / 11 / 0.76 / 5
[62] / 2QUX / Pseudomonas phage PP7 coat protein (125+125) / hairpin RNA (25) / 2.4 / AB / C / 1754 / 801 / 953 / 35 / 11 / 38 / 29 / 22 / 29 / 28 / 35 / 26 / 5 / 0.77 / 8
[63] / 2R8S / synthetic FAB (214+224) / ribozyme (159) / 2.0 / LH / R / 2510 / 1194 / 1316 / 42 / 27 / 53 / 33 / 29 / 22 / 48 / 40 / 25 / 2 / 0.71 / 22
[64] / 2XD0 / P. atrosepticum ToxN (171) / P. atrosepticum ToxI (36) / 3.0 / A / G / 1887 / 882 / 1005 / 35 / 15 / 59 / 28 / 29 / 24 / 39 / 36 / 8 / 3 / 0.53 / 6
[65] / 2Y8W / Endoribonuclease Cse3 (215) / hairpin RNA (20) / 1.8 / A / B / 3258 / 1528 / 1730 / 50 / 17 / 46 / 28 / 30 / 27 / 51 / 51 / 44 / 20 / 0.72 / 3
[66] / 2YKG / RIG-I (696) / dsRNA (10+10) / 2.5 / A / CD / 2150 / 985 / 1165 / 45 / 16 / 70 / 35 / 22 / 24 / 31 / 39 / 13 / 3 / 0.68 / 19
[67] / 2ZI0 / TAV2b (75+75) / siRNA (21+21) / 2.8 / AB / CD / 4574 / 2341 / 2234 / 54 / 39 / 44 / 17 / 18 / 23 / 39 / 43 / 41 / 43 / 0.70 / 3
[68] / 2ZKO / NS1 protein of influenza A (73+73) / A-form dsRNA (21+21) / 1.7 / AB / CD / 2466 / 1238 / 1228 / 34 / 20 / 65 / 36 / 16 / 31 / 40 / 47 / 16 / 18 / 0.62 / 6
[69] / 3A6P / Exp-5:RanGTP (1024+13+216) / pre-microRNA (24+24) / 2.9 / ABC / DE / 4223 / 2043 / 2180 / 77 / 34 / 52 / 37 / 19 / 19 / 35 / 39 / 14 / 18 / 0.53 / 17
[70] / 3BSN / Norwalk virus polymerase (510) / RNA (8+9) / 1.8 / A / PT / 3112 / 1448 / 1663 / 71 / 17 / 59 / 27 / 20 / 22 / 38 / 43 / 22 / 9 / 0.61 / 7
[71] / 3BT7 / Methyltransferase TrmA (369) / T-arm analogue (19) / 2.4 / A / C / 2230 / 982 / 1249 / 42 / 12 / 48 / 33 / 32 / 32 / 47 / 53 / 30 / 7 / 0.58 / 8
[72] / 3DD2 / Thrombin (258) / 26-mer RNA (26) / 1.9 / H / B / 1823 / 892 / 931 / 26 / 15 / 44 / 28 / 20 / 25 / 35 / 48 / 17 / 7 / 0.70 / 7
[73] / 3DH3 / RluF (290) / 23S RNA (22) / 3.0 / B / F / 3425 / 1664 / 1761 / 56 / 18 / 42 / 27 / 38 / 45 / 60 / 71 / 44 / 19 / 0.67 / 4
[74] / 3EQT / Helicase DHX58 (145) / dsRNA (8) / 2.0 / AB / CD / 2706 / 1216 / 1490 / 48 / 16 / 66 / 35 / 33 / 40 / 38 / 52 / 24 / 8 / 0.69 / 5
[75] / 3FTE / Methyltransferase KsgA (249) / rRNA (22+22) / 3.0 / A / CD / 837 / 429 / 407 / 17 / 13 / 63 / 37 / 7 / 9 / 15 / 24 / 2 / 3 / 0.46 / 24
[76] / 3IAB / RNases P/MRP (158+140) / RNase MRP P3 domain (46) / 2.7 / AB / R / 5088 / 2387 / 2701 / 81 / 29 / 62 / 32 / 34 / 32 / 55 / 60 / 35 / 11 / 0.70 / 3
[77] / 3KS8 / Polymerase cofactor VP35 (184+184) / dsRNA (18+18) / 2.4 / AB / EF / 1664 / 799 / 864 / 32 / 12 / 54 / 35 / 19 / 26 / 34 / 46 / 11 / 10 / 0.59 / 9