Computational Structural Biology Lab
Source: http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php Parent: http://www.csb.iitkgp.ac.in/
Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur
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PRDBv3.0
Click here to download the PRDBv3.0 dataset.
Each folder contains the protein-RNA complex, the unbound structure of protein and/or RNA (wherever available) along with the transformed coordinates of unbound protein and/or RNA subunits superposed with the bound subunits. The subunits have been filtered and only chains of interest are retained in the PDB files.
Dataset of protein-RNA binding affinity benchmark.
Pfam domain details on protein-RNA docking benchmark version 3.0.
Protein-RNA docking benchmark dataset GitHub repository.
Table S1: A non-redundant docking benchmark dataset of protein-RNA complexes.
| Bounda | Unbound (PDB ID)a | BSA (Å)b | RMSD (Å) | GDT_TS | LGA_S | Category | |||||||
| PDB ID | Protein | RNA | Protein | RNA | Cα-rmsdc | P-rmsdd | i-rmsde | ||||||
| Cα | P | Cα+P | |||||||||||
| I. Unbound-Unbound cases (27) | |||||||||||||
| (A) Complexes with tRNA (13) | |||||||||||||
| 1ASY (A:R) | S. cerevisiae aspartyl-tRNA synthetase | tRNA-Asp | 1EOV (A) | 2TRA (A) | 4430 | 1.5 | 4.9 | 1.3 | 3.3 | 2.3 | 85.4 | 92.8 | R |
| 1B23 (P:R) | T. aquaticus EF-TU | E. coli tRNA-Cys | 1TUI (A) | 1U0B* (A) | 2616 | 10 | 7.2 | 13.3 | 13 | 13.2 | 50.3 | 47.7 | F |
| 1C0A (A:B) | E. coli aspartyl-tRNA synthetase | tRNA-Asp | 1EQR (A) | 1EFW* (C) | 4504 | 1.6 | 1.8 | 1.6 | 1.8 | 1.7 | 84.0 | 92.0 | S |
| 1QTQ (A:B) | E. coli glutaminyl-tRNA synthetase | tRNA-Gln | 1NYL (A) | 3KNH* (Y) | 5202 | 1.6 | 4.8 | 1.8 | 6.4 | 4.0 | 86.7 | 93.0 | S |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 3430 | 1.2 | 4.6 | 1.3 | 4.1 | 2.5 | 77.1 | 68.4 | R |
| 2DRB (A:B) | A. fulgidus CCA-adding enzyme | tRNAmini CCA | 1UET (A) | 3Q1Q* (C) | 3198 | 1.1 | 3.4 | 1.8 | 4.2 | 2.5 | 86.8 | 87.8 | S |
| 2FMT (A:C) | E. coli methionyl-tRNAfmet transformylase | tRNA-fmet | 1FMT (A) | 3CW6 (A) | 2940 | 1.2 | 2.3 | 0.9 | 2.5 | 1.7 | 91.2 | 96.1 | R |
| 2ZZM (A:B) | M. jannaschii tRNA (guanine(37)-N1)-methyltransferase Trm5b | tRNA-Leu | 2YX1 (A) | 1WZ2* (C) | 4523 | 15.1 | 4.6 | 20 | 6.4 | 12.9 | 74.5 | 73.9 | F |
| 3HL2 (AA'BB':E) | H. sapiens selenium transferase | tRNA-Sec | 3BC8 (AA'A''A''') | 3RG5 (A) | 2186 | 0.6 | 5.2 | 1.3 | 6.0 | 4.3 | 98.0 | 98.9 | R |
| 3VJR (A:B) | E. coli peptidyl-tRNA hydrolase | tRNA CCA-acceptor | 2PTH (A) | 1NJM* (5) | 1354 | 0.8 | 3.7 | 0.8 | 3.8 | 2.0 | 95.9 | 97.9 | R |
| 5X6B (IJEF:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 3WKR (ABCD) | 2ZZN* (C) | 4240 | 0.6 | 3.2 | 1.2 | 6.4 | 3.5 | 99.1 | 99.6 | R |
| 6LVR (C:D) | A. thaliana PRORP1 | yeast tRNA-Phe | 4G24 (A) | 1I9V (A) | 1055 | 3.4 | 1.3 | 4.4 | 1.1 | 4.0 | 70.3 | 67.3 | F |
| 7YSE (AC:E) | E. coli Glycine--tRNA | tRNA-Gly | 7EIV (AC) | 7F36* (E) | 9045 | 3.5 | 6.0 | 4.6 | 5.9 | 4.7 | 82.4 | 80.6 | F |
| (B) Ribosomal proteins (4) | |||||||||||||
| 1DFU (P:MN) | E. coli ribosomal protein L25 | 5s rRNA | 1B75 (A) | 364D (CB) | 1690 | 3.0 | 5.3 | 3.0 | 4.4 | 3.7 | 73.4 | 70.4 | F |
| 1FEU (A:BC) | T. thermophilus ribosomal protein L5 | 5s rRNA | 2J01 (Z) | 364D (BC) | 1595 | 2.1 | 3.3 | 2.4 | 2.8 | 2.6 | 82.1 | 80.7 | S |
| 1MMS (A:C) | T. maritima ribosomal protein L11 | 23S rRNA fragment | 2K3F (A) | 3I9C* (A:1080-1129) | 2455 | 3.5 | 1.6 | 4.1 | 1.6 | 3.3 | 65.2 | 62.3 | F |
| 3IEV (A:D) | A. aeolicus GTPase era | 16S rRNA | 7C1O (A) | 1SDR (B) | 2273 | 0.5 | 7.6 | 0.5 | 8.4 | 4.5 | 98.7 | 99.5 | R |
| (C) Duplex RNA (6) | |||||||||||||
| 1OOA (A:C) | M. musculus NF-kappaB p50 | aptamer RNA | 1LE5 (B) | 2JWV* (A) | 1909 | 6.2 | 6.7 | 5.5 | 7.0 | 6.3 | 64.1 | 62.7 | F |
| 1R3E (A:C) | T. maritime pseudouridine synthase TruB | tRNA fragment | 1ZE1 (A) | 1EHZ (A:49-65) | 3680 | 2.0 | 4.9 | 3.3 | 4.9 | 3.6 | 82.9 | 76.4 | F |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 2HFF (AB) | 1HR2 (A) | 2510 | 1.6 | 4.3 | 2.9 | 2.1 | 2.5 | 87.1 | 93.8 | S |
| 3SNP (A:C) | O. cuniculus iron regulatory protein 1 | ferritin H IRE RNA | 2B3Y (A) | 1AQO* (A) | 2872 | 0.7 | 3.8 | 14.5 | 3.3 | 12.8 | 44.2 | 40.2 | F |
| 2OZB (AB:C) † | H. sapiens Ribonucleoprotein | U4snRNA | 2JNB (A) | 2XEB (A) | 2569 | 1.9 | 11.0 | 1.9 | 13.0 | 19.0 | 80.7 | 90.3 | S |
| 7P0V (A:B) | H. sapiens SF3A1 ubiquitin-like domain | U1 snRNA SL-4 | 7P08 (A) | 8ID2* (C) | 1210 | 1.5 | 1.1 | 1.7 | 0.9 | 1.4 | 87.6 | 94.3 | S |
| (D) Single-stranded RNA (4) | |||||||||||||
| 1JBS (A:C) | A. restrictus restrictocin | SRD RNA analogue | 1AQZ (A) | 1Q9A (A) | 1310 | 0.7 | 3.4 | 0.6 | 3.2 | 1.9 | 97.0 | 98.9 | R |
| 1WSU (A:E) | M. thermoacetica elongation factor Sel B | SECIS RNA | 1LVA (A) | 2RLU (A) | 940 | 0.7 | 4.2 | 0.5 | 1.1 | 0.8 | 98.0 | 98.5 | R |
| 1ZBH (AD:E) | H. sapiens exonuclease ERI1 | histone mRNA | 1ZBU (AD) | 1JU7 (A) | 1760 | 0.6 | 3.6 | 0.6 | 3.4 | 2.0 | 49.6 | 49.8 | R |
| 2BH2 (A:C) | E. coli methyltransferase Rum A | 23S rRNA | 1UWV (A) | 1JZX* (A:1915-1951) | 4491 | 1.4 | 9.8 | 0.7 | 11.0 | 6.0 | 86.0 | 93.5 | R |
| II. Unbound-Bound (160) | |||||||||||||
| (A) Complexes with tRNA (25) | |||||||||||||
| 1F7U (A:B) | S. cerevisiae arginyl-tRNA synthetase | tRNA-Arg | 1BS2 (A) | 5767 | 2.0 | 2.2 | 79.2 | 75.1 | S | ||||
| 1H3E (AA':B) | T. thermophilus tyrosyl-tRNA synthetase | tRNA-Tyr | 1H3F (AB) | 3758 | 7.7 | 4.5 | 68.3 | 62.6 | F | ||||
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 2480 | 1.0 | 0.9 | 88.6 | 94.5 | R | ||||
| 1J1U (AA':B) | M. jannaschii tyrosyl-tRNA synthetase | tRNA-Tyr | 1U7D (AB) | 2240 | 1.3 | 0.8 | 73.5 | 71.6 | R | ||||
| 1N78 (A:C) | T. thermophilus glutamyl-tRNA synthetase | tRNA-Glu | 1J09 (A) | 4510 | 1.9 | 1.4 | 86.4 | 92.4 | R | ||||
| 1QF6 (A:B) | E. coli threonyl-tRNA synthetase | tRNA-Thr | 1EVL (A) | 4602 | 0.8 | 0.7 | 96.6 | 98.5 | R | ||||
| 1SER (AB:T) | T. thermophilus seryl-tRNA synthetase | tRNA-Ser | 1SES (AB) | 2290 | 1.7 | 2.4 | 91.7 | 95.9 | S | ||||
| 1U0B (B:A) | E. coli cysteinyl-tRNA synthetase | tRNA-Cys | 1LI5 (B) | 4560 | 0.7 | 1.0 | 97.7 | 98.9 | R | ||||
| 1VFG (B:D) | A. aeolicus CCA-adding enzyme | tRNA | 4WBY (A) | 1664 | 1.6 | 1.4 | 90.8 | 95.1 | R | ||||
| 2AZX (AA':C) | H. sapiens tryptophanyl-tRNA synthetase | tRNA-Trp | 1R6U (AB) | 2130 | 0.8 | 0.6 | 91.5 | 96.5 | R | ||||
| 2FK6 (A:R) | B. subtilis RNase Z | tRNA-Thr | 1Y44 (A) | 1530 | 0.7 | 0.8 | 97.6 | 98.8 | R | ||||
| 3ADB (A:C) | M. jannaschii O-phosphoseryl-tRNA kinase | tRNA-Sec | 3A4M (A) | 3099 | 22.4 | 27.3 | 72.8 | 70.2 | F | ||||
| 3AMT (A:B) | A. fulgidus agmatinylcytidine synthetase TiaS | tRNA-Ile | 3AU7 (A) | 3821 | 0.8 | 0.7 | 95.6 | 93.6 | R | ||||
| 4YCP (A:B) | E. coli tRNA-dihydrouridine synthase C | tRNA-Trp | 4BFA (A) | 2151 | 0.4 | 6.8 | 99.8 | 99.9 | F | ||||
| 4YVJ (AB:C) | H. influenzae tRNA methyltransferase D | tRNA | 3AXZ (AA') | 2313 | 0.7 | 1.3 | 96.0 | 98.4 | R | ||||
| 5HR7 (A:D) | E. coli RNA methyltransferaseRlmN | tRNA-Glu | 3RFA (A) | 3450 | 1.4 | 1.3 | 93.7 | 96.7 | R | ||||
| 5B63 (A:B) | E.coli arginyl-tRNA synthetase | tRNA-Arg | 5YYM (A) | 3360 | 1.2 | 1.5 | 85.6 | 90.9 | S | ||||
| 5T8Y (B:X) | B. subtilis subsp. epoxyqueuosine reductase | anticodon stem loop of tRNA-Tyr | 5D08 (A) | 697 | 0.4 | 0.3 | 96.0 | 96.6 | R | ||||
| 5WT1 (A:C) | P. abyss Trm5a | tRNA Phe | 5HJI (A) | 4824 | 11.5 | 12.1 | 69.6 | 73.2 | F | ||||
| 5ZW4 (A:D) | B. subtilis subsp. TrmR | tRNA fragment | 5ZW3 (A) | 762 | 0.6 | 0.9 | 98.2 | 99.3 | R | ||||
| 7E8O (AB:X) | P. bacterium PRORP | pre-tRNA-His | 7E8K (AB) | 801 | 1.8 | 1.0 | 89.0 | 92.6 | R | ||||
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (AA'BB') | 7115 | 1.5 | 7.9 | 90.4 | 94.0 | F | ||||
| 7MJW (A:M) | B. uniformis methylated MiaB | tRNA | 7MJZ (A) | 2677 | 1.4 | 1.5 | 88.2 | 93.9 | S | ||||
| 8H1B (A:C) | S. aureus rRNA methylase YtqB | tRNA | 8H1A (A) | 1397 | 0.9 | 1.9 | 95.0 | 97.6 | S | ||||
| 8JOZ (A:B) | E. coli CmoM | tRNA-Ser | 4HTF (A) | 1906 | 0.6 | 1.1 | 94.4 | 95 | R | ||||
| (B) Ribosomal proteins (4) | |||||||||||||
| 1G1X (ABC:DE) † | T. thermophilus ribosomal proteins S6, S15, S18 | 16S rRNA | 1CQM (A) | 4945 | 0.9 | 1.1 | 93.1 | 95.1 | R | ||||
| 1SDS (C:FF') | M. jannaschii 50S ribosomal protein L7Ae | box H/ACA sRNA | 1XBI (A) | 1200 | 0.3 | 0.4 | 100.0 | 100.0 | R | ||||
| 2HW8 (A:B) | T. thermophilus ribosomal protein L1 | mRNA | 1AD2 (A) | 2401 | 6.7 | 5.1 | 64.6 | 47.4 | F | ||||
| 5WTY (A:C) | S. cerevisiae nucleolar protein 9 | 18s rRNA | 5SVD (B) | 3205 | 2.5 | 2.6 | 75.8 | 80.2 | S | ||||
| (C) Duplex RNA (51) | |||||||||||||
| 1MSW (D:R) | Phage T7 RNA polymerase | RNA transcript | 1ARO (P) | 1830 | 3.5 | 3.5 | 57.1 | 54.1 | F | ||||
| 1N35 (A:BC) | Reovirus polymerase | dsRNA | 1MUK (A) | 3240 | 0.5 | 0.9 | 99.3 | 99.7 | R | ||||
| 1Q2R (AB:E) | Z. mobilis guanine transglycosylase | 20-mer tRNA fragment | 1R5Y (AA') | 3006 | 0.6 | 1.6 | 98.0 | 99.0 | S | ||||
| 1WNE (A:BC) | Foot-and-mouth disease virus polymerase | template-primer RNA decanucleotide | 1U09 (A) | 3080 | 0.7 | 0.6 | 97.2 | 99.0 | R | ||||
| 1YVP (B:EFH) | F. laevis Ro autoantigen | Y RNA | 1YVR (A) | 4207 | 1.4 | 1.3 | 90.6 | 95.2 | R | ||||
| 1ZBI (A:CD) | B. halodurans RNase H | A form RNA | 1ZBF (A) | 1675 | 0.6 | 0.6 | 98.7 | 99.5 | R | ||||
| 2AZ0 (AB:CD) | Flock house virus B2 | siRNA | 2B9Z (AB) | 2264 | 1.3 | 1.0 | 85.5 | 93.3 | R | ||||
| 2BGG (A:PQ) | A. fulgidus PIWI | siRNA | 1W9H (A) | 2240 | 0.9 | 0.8 | 96.5 | 98.2 | R | ||||
| 2EZ6 (AB:CD) | A. aeolicus RNase III | 28-mer RNA | 1JFZ (AB) | 5193 | 1.0 | 0.8 | 95.5 | 84.9 | R | ||||
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 990 | 1.9 | 1.5 | 77.4 | 78.3 | S | ||||
| 2GJW (AB:EFH) | A. fulgidus splicing endonuclease | bulge-helix-bulge RNA | 1R0V (AB) | 3243 | 1.0 | 1.0 | 83.0 | 91.7 | R | ||||
| 2GXB (A:EF) | H. sapiens Z alpha domain of adenosine deaminase | dsRNA | 1QGP (A) | 768 | 1.1 | 0.7 | 87.9 | 90.9 | R | ||||
| 2QUX (AB:C) | Pseudomonas phage PP7 coat protein | hairpin RNA | 2QUD (AB) | 1754 | 0.9 | 0.5 | 96.9 | 98.4 | R | ||||
| 2Y8W (A:B) | T. thermophilus endoribonuclease Cse3 | hairpin RNA | 1WJ9 (A) | 3258 | 1.1 | 3.1 | 95.5 | 97.3 | F | ||||
| 2ZKO (AB:CD) | NS1 protein of influenza A | A-form dsRNA | 2Z0A (AB) | 2466 | 0.6 | 0.8 | 97.7 | 98.8 | R | ||||
| 3A6P (AC:DE) | H. sapiens exp-5:Ran GTP | pre-microRNA | 5YU6 (AB) | 4223 | 1.2 | 1.4 | 91.8 | 96.4 | R | ||||
| 3BSN (A:PT) | Norwalk virus polymerase | synthetic RNA | 1SH3 (A) | 3111 | 1.3 | 1.9 | 90.9 | 95.2 | S | ||||
| 3DD2 (H:B) | H. sapiens thrombin | 26-mer RNA | 1JOU (D) | 1822 | 0.6 | 0.5 | 96.5 | 98.1 | R | ||||
| 3EQT (AB:CD) | H. sapiens helicase DHX58 | dsRNA | 2W4R (AA') | 2705 | 1.2 | 1.2 | 47.9 | 42.5 | R | ||||
| 3FTE (A:CD) | A. aeolicus methyltransferase KsgA | rRNA | 3FTD (A) | 836 | 1.4 | 1.1 | 89.7 | 94.9 | R | ||||
| 3KS8 (AB:EF) | R. ebolavirus polymerase cofactor VP35 | dsRNA | 3KS4 (AB) | 1663 | 0.6 | 0.4 | 49.8 | 50.1 | R | ||||
| 3MOJ (B:A) | B. subtilis helicase dbpA | E.coli 23S rRNA fragment | 2G0C (A) | 1758 | 1.0 | 1.0 | 94.5 | 97.6 | R | ||||
| 3O3I (X:A) | H. sapiens Hiwi1 PAZ domain | piRNA | 2L5C (A) | 923 | 2.1 | 2.7 | 79.0 | 84.5 | S | ||||
| 3OIJ (AB:C) | S. cerevisiae methyltransferase | SSU rRNA | 3OII (AB) | 2070 | 0.8 | 1.7 | 97.0 | 98.5 | S | ||||
| 3OL6 (A:BCD) | Poliovirus polymerase | synthetic RNA | 1RA6 (A) | 4174 | 0.8 | 1.1 | 94.9 | 97.8 | R | ||||
| 3RW6 (A:H) | H. sapiens nuclear RNA export factor 1 | CTE RNA | 3RW7 (A) | 2699 | 13.5 | 19.0 | 66.4 | 64.4 | F | ||||
| 3ZC0 (AA'BB'CC'DD':MM') | A. fulgidus C3PO | duplex RNA | 3ZC1 (ABCDEFGH) | 2324 | 0.5 | 0.5 | 98.6 | 99.2 | R | ||||
| 4ERD (AB:CD) | T. thermophila p65 C-terminal domain | stem IV of telomerase RNA | 4EYT (AB) | 3280 | 1.5 | 1.2 | 47.0 | 46.5 | R | ||||
| 4FVU (A:BC) | Lassa virus exonuclease | dsRNA | 3Q7C (A) | 1240 | 1.0 | 0.7 | 97.2 | 98.5 | R | ||||
| 4IG8 (A:BC) | H. sapiens oligoadenylate synthetase 1 | dsRNA | 1PX5 (A) | 2914 | 2.4 | 2.8 | 79.0 | 74.4 | S | ||||
| 4ILL (AB:RC) | S. solfataricus endoribonuclease Cas6 | CRISPR RNA | 4ILR (AA') | 7074 | 0.9 | 0.9 | 96.3 | 98.1 | R | ||||
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 10845 | 29.6 | 22 | 45.6 | 43.1 | F | ||||
| 5ED1 (A:BC) | H. sapiens ADAR2 | S. cerevisiae dsRNA | 1ZY7 (A) | 2403 | 1.1 | 2.3 | 95.4 | 97.5 | S | ||||
| 5F5H (A:C) | M. musculus Roquin-1 | Ox40 3'-UTR | 4QI0 (A) | 1618 | 0.5 | 0.6 | 99.2 | 99.6 | R | ||||
| 5WTK (A:B) | L. shahii CRISPR-associated endoribonuclease C2c2 | crRNA | 5WTJ (A) | 8811 | 4.9 | 4.0 | 60.5 | 65.2 | F | ||||
| 5ZQ8 (A:D) | S. pneumoniae RlmCD | 23S rRNA U747 stemloop | 5XJ1 (A) | 1992 | 1.5 | 1.2 | 86.4 | 93.7 | R | ||||
| 6D12 (B:C) | H. sapiens xRRM domain of human Larp7 | 7SK stem-loop 4 RNA | 5KNW (A) | 1428 | 2.1 | 1.6 | 79.1 | 88.2 | S | ||||
| 6DCB (A:B) | H. sapiens methylphosphate capping enzyme | 5' end of 7SK RNA | 5UNA (A) | 697 | 0.7 | 0.3 | 95.0 | 95.8 | R | ||||
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 986 | 7.9 | 2.0 | 72.5 | 74.7 | S | ||||
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 3ZQI (AB) | 1702 | 1.7 | 2.0 | 82.1 | 91.0 | S | ||||
| 6PZQ (AB:IJ) | HRSV matrix M2-1 | Gene-End RNA | 6G0Y (AC) | 668 | 0.9 | 0.5 | 97.6 | 99.2 | R | ||||
| 6RTI (A:X) | H. sapiens GCPII | A9gRNA aptamer | 2C6C (A) | 3147 | 0.4 | 0.6 | 99.6 | 99.9 | R | ||||
| 6ZDP (A:B) | C. tropicalis telomerase reverse transcriptase | TWJ fragment of telomeric RNA | 6ZD6 (A) | 2629 | 4.1 | 8.4 | 60.7 | 62.0 | F | ||||
| 7KFN (AD:BC) | H. sapiens ADAR2 | Gli1 8AZ 23mer dsRNA | 1ZY7 (AB) | 2724 | 0.9 | 1.6 | 97.2 | 98.6 | S | ||||
| 7KKV (A:B) | A. halodurans OapB protein | OLE RNA target | 7K9B (A) | 1365 | 0.7 | 0.7 | 88.3 | 89.9 | R | ||||
| 7OG0 (A:EE') | H. influenzae SapA | dsRNA | 8TV8 (A) | 597 | 3.0 | 2.1 | 65.4 | 59.7 | S | ||||
| 7OM6 (A:DF) | T. asigna virus RdRP domain | RNA oligonucleotide | 7OM2 (A) | 6642 | 0.9 | 1.4 | 96.6 | 98.1 | R | ||||
| 7XD8 (A:BC) | Dengue virus 2 NS5 | 30-mer RNA | 6KR2 (A) | 3539 | 3.7 | 5.2 | 61.5 | 64.8 | F | ||||
| 7XWZ (A:CD) | SARS-CoV-2N-NTD nucleoprotein | dsRNA | 7VNU (A) | 811 | 1.0 | 2.2 | 96.9 | 98.1 | S | ||||
| 7ZLQ (A:DE) | H. Sapiens ADAR1-dsRBD3 | dsRNA | 2MDR (A) | 784 | 1.3 | 0.6 | 79.8 | 83.8 | R | ||||
| 8AF0 (AB:CD) | H. Sapiens Angiogenin | dsRNA | 5M9T (AB) | 1068 | 0.7 | 0.4 | 98.8 | 99.4 | R | ||||
| (D) Single-stranded RNA (80) | |||||||||||||
| 1AV6 (A:B) | Vaccinia virus cap-specific mRNA methyltransferase | M7G capped RNA | 1B42 (A) | 844 | 0.5 | 0.4 | 99.1 | 99.6 | R | ||||
| 1C9S (L:W1-7) | G. stearothermophilus TRAP | ssRNA | 2EXT (A) | 1027 | 0.3 | 0.2 | 100.0 | 100.0 | R | ||||
| 1CVJ (A:M) | H. sapiens poly(A)-binding protein | polyA | 4F25 (A) | 2822 | 2.7 | 3.9 | 93.4 | 93.9 | F | ||||
| 1G2E (A:B) | H. sapiens RRM domain of the HuD protein | class II ARE fragment | 4EGL (A) | 2776 | 0.9 | 0.6 | 49.8 | 49.8 | R | ||||
| 1K8W (A:B) | E. coli pseudouridine synthase B | T stem-loop RNA | 1R3F (A) | 2973 | 1.9 | 1.3 | 80.8 | 90.3 | R | ||||
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 3026 | 0.6 | 0.5 | 81.9 | 91.8 | R | ||||
| 1M5O (C:B) | H. sapiens U1 Snp A | hairpin ribozyme | 1OIA (A) | 1770 | 1.2 | 0.9 | 96.6 | 98.1 | R | ||||
| 1M8V (AM:O) | P. abyssi Sm | uridine heptamer | 1H64 (AM) | 1290 | 0.6 | 0.4 | 62.2 | 61.2 | R | ||||
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 2110 | 0.8 | 0.7 | 90.9 | 96.0 | R | ||||
| 1UVI (A:D) | phi6 RNA polymerase | 6-mer RNA | 1HHS (A) | 1814 | 0.2 | 0.2 | 100.0 | 100.0 | R | ||||
| 1WPU (A:C) | B. subtilis HutP antitermination protein | hut mRNA | 1WPV (A) | 1360 | 0.2 | 0.2 | 100.0 | 100.0 | R | ||||
| 2A8V (B:E) | E. coli RHO | Cytosine rich RNA | 1A8V (B) | 720 | 1.0 | 1.6 | 94.7 | 97.7 | S | ||||
| 2ASB (A:B) | M. tuberculosis Nus A antiterminator | BoxC rRNA | 1K0R (A) | 2320 | 1.1 | 0.8 | 91.8 | 96.4 | R | ||||
| 2GIC (A:R) | VSV nucleocapsid | viral genomic RNA | 2QVJ (A) | 2000 | 1.3 | 0.9 | 91.9 | 95.7 | R | ||||
| 2IX1 (A:B) | E. coli RNase II | polyA | 2IX0 (A) | 4160 | 1.6 | 0.9 | 86.2 | 93.3 | R | ||||
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 2JE6 (AB) | 1533 | 0.3 | 0.3 | 99.8 | 99.9 | R | ||||
| 2JLU (A:C) | Dengue virus serine protease subunit NS3 | ssRNA | 2JLQ (A) | 1925 | 2.1 | 2.8 | 74.3 | 78.1 | S | ||||
| 2PY9 (B:E) | H. sapiens poly(rC)-binding protein 2 | human telomeric RNA | 2JZX(A:1-73) | 1060 | 1.4 | 1.6 | 85.5 | 92.0 | R | ||||
| 2Q66 (A:X) | S. cerevisiae poly(A) polymerase | polyA | 2HHP (A) | 1811 | 1.9 | 2.1 | 85.0 | 91.5 | S | ||||
| 2R7R (A:X) | Rotavirus polymerase VP1 | RNA | 2R7Q (A) | 1955 | 0.2 | 1.9 | 98.7 | 99.3 | S | ||||
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 1389 | 4.1 | 3.1 | 71.5 | 65.5 | F | ||||
| 2XNR (A:C) | S. cerevisiae Nab3-RRM | UCUU recognition sequence | 2XNQ (A) | 926 | 1.0 | 1.2 | 94.3 | 97.4 | R | ||||
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 2XZP (A) | 2006 | 6.2 | 5.0 | 57.2 | 54.2 | F | ||||
| 3AEV (B:C) | P. horikoshii Dim2p | P. horikoshii 16S rRNA fragment | 2E3U (A) | 2416 | 0.7 | 0.5 | 97.4 | 99.0 | R | ||||
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 2467 | 0.6 | 0.5 | 98.5 | 99.3 | R | ||||
| 3D2S (A:E) | H. sapiens MBNL1 ZnF3/4 | pre-mRNA | 3D2Q (A) | 569 | 0.8 | 0.6 | 97 | 98.7 | R | ||||
| 3MDG (AB:C) | H. sapiens CFI(m)25 | pre-mRNA | 3BAP (AA') | 1069 | 0.5 | 0.9 | 96.5 | 98.1 | R | ||||
| 3NMR (A:B) | H. sapiens CUG-binding protein 1 | UGU-rich mRNA | 2DHS (A) | 1096 | 2.7 | 2.2 | 43.0 | 39.7 | S | ||||
| 3O8C (A:C) | HCV NS3 helicase | polyU | 3O8B (A) | 1909 | 1.0 | 1.1 | 94.6 | 97.5 | R | ||||
| 3PF4 (B:R) | B. subtilis CspB | ssRNA | 1CSP (A) | 963 | 0.5 | 0.4 | 98.5 | 99.4 | R | ||||
| 3QJJ (A:Q) | P. horikoshii RAMP Protein | CRISPR repeat RNA | 3UFC (X) | 3191 | 1.0 | 1.0 | 96 | 98.3 | R | ||||
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 1471 | 1.1 | 0.8 | 92.3 | 96.3 | R | ||||
| 4E78 (A:PT) | HCV polymerase | RNA primer-template pair | 4E76 (A) | 2100 | 0.7 | 0.8 | 98.4 | 99.4 | R | ||||
| 4H5P (AB:E) | Rift valley fever virus nucleocapsid | polyU | 3LYF (AB) | 4482 | 0.9 | 2.1 | 42.5 | 42.6 | S | ||||
| 4HOR (A:X) | H. sapiens IFIT | polyC | 4HOQ (A) | 1747 | 3.1 | 2.4 | 68.7 | 72.5 | S | ||||
| 4J7M (A:B) | M. musculus Dom3Z | polyU | 4J7N (A) | 1268 | 0.3 | 0.3 | 99.7 | 99.9 | R | ||||
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 7842 | 10.5 | 7.1 | 30.1 | 26.1 | F | ||||
| 4MDX (AB:C) | B. subtilis mRNA interferase MazF | mRNA | 1NE8 (AA') | 2127 | 0.7 | 1.6 | 98.4 | 86.4 | S | ||||
| 4N2Q (A:B) | B. distachyon thylakoid assembly 8 | Zm4 13-mer RNA | 4ME2 (A) | 814 | 2.3 | 1.3 | 78.6 | 82.3 | R | ||||
| 4QU6 (A:B) | H. sapiens GRSF1 | synthetic RNA | 2LMI (A) | 696 | 2.5 | 2.4 | 80.8 | 80.6 | S | ||||
| 5DET (AB:PQ) | H. sapiens RBPMS | CAC containing ssRNA | 5CYJ (AB) | 2137 | 1.2 | 1.6 | 46.9 | 47.6 | S | ||||
| 5EIM (A:C) | S. pombe YTH domain of spMmi1 | synthetic RNA | 5H8A (A) | 1529 | 0.6 | 1.3 | 98.2 | 99.3 | R | ||||
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 5EL3 (AB) | 2313 | 1.5 | 2.9 | 47.7 | 49.1 | S | ||||
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 1Q7F (A) | 1639 | 0.5 | 0.8 | 97.0 | 97.6 | R | ||||
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE (A) | 1711 | 0.4 | 0.2 | 97.0 | 97.2 | R | ||||
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5D0U (A) | 2287 | 2.4 | 2.2 | 72.1 | 76.4 | S | ||||
| 5SZE (A:C) | A. aeolicus Hfq-RNA | PolyU | 5SZD (A) | 502 | 1.1 | 0.5 | 94.1 | 95.1 | R | ||||
| 5V7C (B:C) | H. sapiens LARP1-unique domain DM15 | 5'TOP motif | 5V87 (A) | 1238 | 0.4 | 0.5 | 96.9 | 97.2 | R | ||||
| 5W0M (A:H) | H. sapiens TUT7 catalytic module | PolyU | 5W0B (A) | 1734 | 0.9 | 1.1 | 93.4 | 97.2 | R | ||||
| 5WWX (A:C) | H. sapiens KH2 domain of MEX-3C | 5-mer RNA | 5WWZ (A) | 1380 | 0.8 | 0.9 | 92.9 | 96.8 | R | ||||
| 5ZSC (A:C) | M. mulatta toll-like receptor 7 | CCUUCA RNA | 6IF5 (A) | 1227 | 0.5 | 0.5 | 99.7 | 99.8 | R | ||||
| 6A4E (A:B) | C. psychrerythraea oligoribonuclease | U-rich RNA | 6A4D (A) | 759 | 0.5 | 0.4 | 98.6 | 99.5 | R | ||||
| 6A6J (A:B) | D. rerio cold shock domain of Ybx1 | 6mer m5C RNA | 6LMS (A) | 1167 | 1.2 | 1.2 | 89.2 | 93.9 | R | ||||
| 6GC5 (A:E) | H. sapiens HuR RRM3 | AU-rich RNA | 6GD1 (A) | 1264 | 0.7 | 0.8 | 97.3 | 99.1 | R | ||||
| 6HAU (AB:D) | Herpesvirus saimiri mRNA export factor ICP27 homolog | MRE fragment of PAN RNA | 6HAT (AB) | 994 | 0.6 | 0.2 | 99.7 | 99.8 | R | ||||
| 6I0V (A:B) | D. melanogaster DmTailor | 8-mer RNA | 6I0S (A) | 1380 | 0.6 | 0.9 | 97.5 | 98.5 | R | ||||
| 6L1W (A:C) | M. musculus Zinc finger CCCH-type antiviral protein 1 | CG rich RNA | 3U9G (A) | 1356 | 1.6 | 2.0 | 84.8 | 91.5 | S | ||||
| 6LLB (A:C) | M. psychrophilus MPY-RNase J | 6-mer RNA | 5HAA (A) | 2527 | 0.8 | 0.7 | 97.8 | 99.0 | R | ||||
| 6R9P (A:B) | S. cerevisiae apo Pan2 pseudoubiquitin hydrolase | AAUUAA RNA | 6R9I (A) | 974 | 0.8 | 0.6 | 95.6 | 97.4 | R | ||||
| 6U9X (D:H) | T. brucei MERS1 | G rich RNA | 6NL1 (A) | 2250 | 1.4 | 1.8 | 89.5 | 94.4 | S | ||||
| 6L5N (A:C) | H. sapiens DEAD-box RNA helicase DDX21 | poly(U)-15mer | 6L5M (A) | 1201 | 1.4 | 1.2 | 92.1 | 95.9 | R | ||||
| 6LT7 (AB:C) | H. sapiens RPP20-RPP25 | P3 domain of lncRNA RMRP | 6CWX (AB) | 5371 | 1.6 | 1.6 | 91.0 | 94.8 | S | ||||
| 6U6Y (AD:EH) | H. sapiensSAMHD1 | ribo(CGCCU)-oligonucleotide | 5AO3 (AB) | 1996 | 0.5 | 0.3 | 99.2 | 99.7 | R | ||||
| 6WXY (BC:A) | T. succinifaciens card1 nuclease | cA6-bound | 6WXW (AB) | 2186 | 0.5 | 0.6 | 99.4 | 99.8 | R | ||||
| 6ZOT (A:C) | H. sapiens YTH domain-containing family protein 3 | m6A RNA | 8BS5 (A) | 1352 | 0.6 | 0.5 | 91.6 | 91.8 | R | ||||
| 7C45 (A:D) | T. brucei RNase D ribonuclease | gRNA U12 | 7C42 (A) | 2405 | 2.6 | 4.0 | 87.2 | 88.3 | F | ||||
| 7DOL (A:C) | M. genitalium Ribonuclease R | ssRNA | 7DCY (A) | 2076 | 1.0 | 0.9 | 81.0 | 85 | R | ||||
| 7K5L(A:R) | Ebola virus Matrix protein VP40 | HSP RNA oligonucleotide | 4LDM (A) | 474 | 0.2 | 0.2 | 100.0 | 100.0 | R | ||||
| 7EIU (A:C) | S. pombe meiosis protein mei2 RRM3 | 8mer meiRNA | 7EIO (A) | 2431 | 0.9 | 0.6 | 97.1 | 98.3 | R | ||||
| 7KL3 (A:B) | H1N1 california PA endonuclease | RNA oligomer AG*CAUC | 5CZN (A) | 848 | 0.2 | 0.3 | 98.9 | 98.9 | R | ||||
| 7L6T (A:C) | SARS-CoV-2 Nsp16/10 Heterodimer | mRNA capping | 7C2I (A) | 1120 | 0.6 | 1.0 | 98.7 | 99.4 | R | ||||
| 7V4G (A:D) | H. sapiens RNA demethylase ALKBH5 | m6A-containing ssRNA | 4O61 (A) | 1529 | 0.6 | 0.7 | 92.1 | 93.0 | R | ||||
| 7VSJ (A:B) | M. Musculus MmIMP3-RRM12 | mRNA | 6FQ1 (A) | 830 | 0.5 | 0.5 | 96.8 | 97.5 | R | ||||
| 7VKI (A:B) | H Sapiens ESRP1 Qrrm2 | mRNA | 2DHA (A) | 632 | 1.5 | 1.0 | 81.9 | 84.1 | R | ||||
| 7VKL (A:B) | M. Musculus MmIMP3-KH12 | zipcode RNA | 6GQE (A) | 1227 | 1.1 | 1.3 | 94.0 | 96.5 | R | ||||
| 7Y7Q (AB:CED) | N. Crasa QDE-1 | synthetic RNA | 2J7N (AB) | 3920 | 1.1 | 1.0 | 94.6 | 97.6 | R | ||||
| 8DZK(A:F) | E. Histolytica Dbr1 | bRNAs | 5K71 (A) | 1262 | 0.2 | 0.4 | 100.0 | 100.0 | R | ||||
| 8EDJ (A:R) | M. mulatta APOBEC3G | RA3G-ssRNA-GA | 6P3X (A) | 1692 | 17.7 | 23.2 | 51.5 | 49.6 | F | ||||
| 8AXF (ABCD:Q) | E. Fici nucleocapsid protein | ssRNA | 8AX4 (ABCD) | 10949 | 3.7 | 3.2 | 87.6 | 86.9 | F | ||||
| 8TG4 (A:C) | A. pernix Tpt1 | 2'-OH RNA | 8TG3 (A) | 974 | 0.2 | 0.2 | 97.3 | 97.3 | R | ||||
| III. Bound-Unbound cases (10) | |||||||||||||
| (A) Complexes with tRNA (2) | |||||||||||||
| 2ZM5 (A:C) | E. coli iso-pent-enyl-transferase | tRNA-Phe | 3L0U (A) | 3936 | 4.2 | 6.5 | |||||||
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP* (F) | 4322 | 2.8 | 2.9 | |||||||
| (B) Ribosomal proteins (1) | |||||||||||||
| 6AAX (A:B) | H. sapiens Mitochondrial transcription factor B1 | 12s rRNA | 6AAS (A) | 1758 | 3.9 | 6.1 | |||||||
| (C) Duplex RNA (5) | |||||||||||||
| 1HQ1 (A:B) | E. coli SRP | 4.5S RNA domain IV | 1DUH (A) | 1364 | 38.3 | 30.0 | |||||||
| 1JID (A:B) | H. sapiens SRP19 | SRP RNA | 1D4R (A) | 1436 | 2.6 | 4.0 | |||||||
| 2PJP (A:B) | E. coli SelB | SECIS RNA | 1MFK (A) | 1300 | 2.5 | 3.6 | |||||||
| 3BT7 (A:C) | E. coli methyltransferase TrmA | T-arm analogue | 1EVV (A) | 2230 | 3.1 | 3.5 | |||||||
| 6HTU (ABC:DF) | H. sapiens hStau1 dsRBD3-4 | ARF1 RNA | 6HU6 (AE) | 3840 | 1.6 | 1.6 | |||||||
| (D) Single-stranded RNA (2) | |||||||||||||
| 1LNG (A:B) | M. jannaschii SRP19 | 7S SRP RNA | 1Z43 (A) | 2367 | 2.0 | 2.1 | |||||||
| 2I82 (A:E) | E. coli pseudouridine synthase RluA | tRNA-Phe | 3L0U (A:26-43) | 3018 | 4.2 | 4.7 |
aFour-letter PDB code of the protein-RNA complexes with chain id of the protein and the RNA molecules in the parenthesis.
The first model of each NMR structures (shown in bold) considered for structural alignment.
Symmetry related chains are primed (For example, A' and B' in 3HL2). If the unbound RNA structure is taken from another complex they are marked with * (For example, in 3I9C nucleotides from 1080 to 1129 are considered).
bSurface area buried (BSA) between protein and RNA upon complexation.
crmsd calculated considering the equivalent Cα atoms.
drmsd calculated considering the equivalent phosphorus (P) atoms.
ermsd calculated considering the equivalent interface atoms.
†Complexes for which only single chain is available in the unbound forms. The bound PDB chain used for superposition with unbound PDB chain is underlined in bold font. (e.g. 2OZB AB:C)