Computational Structural Biology Lab
Source: http://www.csb.iitkgp.ac.in/applications/benchmark.php Parent: http://www.csb.iitkgp.ac.in/
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Supplementary Information for Protein RNA benchmark
Each folder contains the protein-RNA complex, the unbound structure of protein and RNA(wherever available;9 cases).
The transformed coordinates of bound and unbound protein subunits computed by DaliLite and that for RNA subunits computed by Gromacs is also available in the folder.
The subunits have been filtered and only chains of interest are retained in the PDB files.
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Click here to download the zipped protein-RNA benchmark
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Table 1. The benchmark dataset of Protein-RNA complexes.
| Complex | Unbound (PDB id) | Interface Area Bb(Å2) | RMSD (Å) | Categoryf | |||||
| PDB ida | Protein | RNA | Protein | RNA | i-rmsdc | c-rmsdd | p-rmsde | ||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1. Unbound-Unbound (9) 1. Complexes with tRNA (3) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1asy (A:R) | Aspartyl-tRNA synthetase | tRNA (Asp) | 1eov (A) | 2tra (A) | 4430 | 1.26 2.30 | 1.49 | 4.9 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1ttt (A:D) | Elongation Factor EF-TU | tRNA (Phe) | 1eft (A) | 4tna (A) | 2890 | 0.67 1.32 | 0.69 | 2.5 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2fmt (A:C) | tRNA-fMet transformylase | tRNA (fMet) | 1fmt (A) | 3cw6 (A) | 2940 | 0.93 1.70 | 1.17 | 2.3 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Ribosomal proteins (1) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1dfu (P:MN) | Ribosomal protein L25 | 5S rRNA | 1b75 (A) | 364d (ABC) | 1690 | 2.99 3.73 | 3.00 | 5.3 | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 3. Duplex RNA (1) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1e7k (A:C) | Spliceosomal protein 15.5K | U4 snRNA | 2jnb (A) | 1mfj (A) | 1300 | 0.98 3.97 | 2.10 | 8.1 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 4. Single-stranded RNA (4) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1jbs (A:C) | Sarcin-like cytotoxin Restrictocin | 29-mer SRD RNA analog | 1aqz (A) | 1q9a (A) | 1310 | 0.59 1.92 | 0.71 | 3.4 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1wsu (A:E) | Elongation factor SelB | SECIS RNA | 1lva (A) | 2rlu (A) | 940 | 0.45 0.77 | 0.70 | 4.6 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1zbh (AD:E) | 3'-Endonuclease Eri1 | Histone mRNA | 1zbu (AD) | 1ju7 (A) | 1760 | 0.62 1.98 | 0.60 | 4.2 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2b6g (A:B) | Vts1p | SRE hairpin RNA | 2d3d (A) | 2b7g (A) | 483 | 0.29 0.89 | 0.90 | 2.47 | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Unbound-Bound (36) 1. Complexes with tRNA (13) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1c0a (A:B) | Aspartyl-tRNA synthetase | tRNA (Asp) | 1eqr (A) | - | 4180 | 1.60 | 1.63 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1f7u (A:B) | Arginyl-tRNA synthetase | tRNA (Arg) | 1bs2 (A) | - | 5140 | 2.17 | 2.00 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1h4s (AB:T) | Prolyl-tRNA synthetase | tRNA (Pro) | 1hc7 (AB) | - | 2480 | 0.95 | 1.02 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1j1u (AA':B) | Tyrosyl-tRNA synthetase | tRNA (Tyr) | 1u7d (AB) | - | 2240 | 0.77 | 1.27 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1n78 (A:C) | Glutamyl-tRNA synthetase | tRNA (Glu) | 1j09 (A) | - | 4510 | 1.44 | 1.87 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1qf6 (A:B) | Threonyl-tRNA synthetase. | tRNA (Thr) | 1evl (A) | - | 4230 | 0.74 | 0.80 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1qtq (A:B) | Glutaminyl-TRNA synthetase | tRNA (Gln) | 1nyl (A) | - | 5200 | 1.85 | 1.62 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1ser (AB:T) | Seryl-tRNA Synthetase | tRNA (Ser) | 1ses (AB) | - | 2290 | 2.44 | 1.69 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1u0b (B:A) | Cysteinyl-tRNA synthetase | tRNA (Cys) | 1li5 (B) | - | 4560 | 0.96 | 0.66 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2azx (AA':C) | Tryptophanyl-tRNA synthetase | tRNA (Trp) | 1r6u (AB) | - | 2130 | 0.59 | 0.81 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2bte (A:B) | Leucyl-tRNA synthetase | tRNA (Leu) | 1obc (A) | - | 3430 | 1.34 | 1.2 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2drb (A:B) | CCA-adding enzyme | tRNA (35-mer) | 1uet (A) | - | 3200 | 1.75 | 1.06 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2fk6 (A:R) | RNase Z | tRNA (Thr) | 1y44 (A) | - | 1530 | 0.83 | 0.74 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2. Ribosomal proteins (2) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1sds (C:FF') | Ribosomal protein L7Ae | box H/ACA sRNA | 1xbi (A) | - | 1200 | 0.37 | 0.33 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2hw8 (A:B) | Ribosomal protein L1 | mRNA | 1ad2 (A) | - | 2330 | 5.06 | 6.67 | - | X |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 3. Duplex RNA (9) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1msw (D:R) | RNA polymerase, phage T7 | 17-nucleotide RNA transcript | 1aro (P) | - | 1830 | 3.55 | 3.5 | - | X |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1r3e (A:CDE) | Pseudo-U synthetase TruB | 17- nucleotide RNA | 1ze1 (A) | - | 3280 | 3.34 | 2.0 | - | X |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1wne (A:BC) | RNA polymerase, FMD virus | template-primer RNA decanucleotide | 1u09 (A) | - | 3080 | 0.62 | 0.70 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1yvp (B:EFH) | Ro autoantigen | Y RNA | 1yvr (A) | - | 3500 | 1.26 | 1.44 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1zbi (A:CD) | RNase H | A form RNA | 1zbf (A) | - | 3210 | 0.63 | 0.56 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2az0 (AB:CD) | Flock House virus protein B2 | siRNA | 2b9z (AB) | - | 1970 | 1.01 | 1.30 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2ez6 (AB:CD) | RNase III | dsRNA | 1jfz (AB) | - | 5190 | 0.77 | 1.00 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2f8s (A:CD) | Argonaute protein | siRNA | 1yvu (A) | - | 990 | 1.53 | 1.90 | - | S |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2gjw (AB:EFH) | Splicing endonuclease | BHB RNA | 1r0v (AB) | - | 2620 | 1.02 | 0.95 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 4. Single-stranded RNA (12) | |||||||||
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1k8w (A:B) | Pseudo-U synthetase TruB | T stem-loop RNA | 1r3f (A) | - | 2610 | 1.27 | 1.90 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1m5o (C:B) | U1 SnpA Ribozyme | Hairpin ribozyme | 1oia (A) | - | 1770 | 0.91 | 1.20 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1m8v (AM:O) | Sm like protein | Uridine heptamer | 1h64 (AM) | - | 1290 | 0.37 | 0.60 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1m8w (A:C) | PH domain | Nre1-19 RNA | 1m8z (A) | - | 2110 | 0.75 | 0.80 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1n35 (A:BC) | RNA polymerase lambda3, reovirus | dsRNA | 1muk (A) | - | 3240 | 0.94 | 0.50 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1wpu (A:C) | Hutp antiterminator | Hut mRNA | 1wpv (A) | - | 1360 | 0.17 | 0.23 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2a8v (B:E) | RHO transcription termin. factor | Cytosine-rich RNA | 1a8v (B) | - | 720 | 1.62 | 1.00 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2asb (A:B) | NusA antiterminator | BoxC rRNA | 1k0r (A) | - | 2320 | 0.82 | 1.08 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2bgg (A:PQ) | PIWI protein | siRNA | 1w9h (A) | - | 2240 | 0.76 | 0.90 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2bh2 (A:C) | Methyltransferase RumA | 23S rRNA | 1uwv (A) | - | 4040 | 0.67 | 1.41 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2gic (A:R) | VSV nucleocapsid | Viral genomic RNA | 2qvj (A) | - | 2000 | 0.88 | 1.30 | - | R |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 2ix1 (A:B) | RNase II | Single-stranded RNA | 2ix0 (A) | - | 4160 | 0.94 | 1.59 | - | S |
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aFour-letter PDB code of the protein-RNA complexes used in the dataset with the chain ID(s) of the protein and the RNA molecules in the parentheses. Structures solved with NMR spectroscopy method are shown in bold. Symmetry-related chains are primed (e.g. A' in 1j1u).
bSurface area buried between protein and RNA upon complexation.
RMSD was calculated over the cC&alpha atoms of the interface residues, while the values in italics include the phosphorus atoms of the interface nucleotides when the corresponding free RNA structure is available; dAll C&alpha atoms of the protein chain; eAll phosphorus atoms of the RNA chain when the unbound structure of the same is available.
fDifferent categories according to the expected difficulty for the protein-RNA docking algorithm: (R) Rigid body, (S)Semi flexible and (X) Full flexible.
\