Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

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.


Click here to download the zipped protein-RNA benchmark


Table 1. The benchmark dataset of Protein-RNA complexes.

Complex

Unbound

(PDB id)

Interface Area Bb2)

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

  1. 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

  1. 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

  1. 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

  1. 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

  1. 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

  1. 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

  1. 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


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.