# Computational Structural Biology Lab

**Source**: http://www.csb.iitkgp.ac.in/applications/affinity.php
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### Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur

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## Protein-RNA affinity Benchmark

**[Click here to download the table in MS Office format](http://www.facweb.iitkgp.ac.in/~rbahadur/affinity.doc)**

**[Click here to download the table in PDF format](http://www.facweb.iitkgp.ac.in/~rbahadur/affinity.pdf)**

**[Click here to download the table in Open Document (GNU/Linux) format](http://www.facweb.iitkgp.ac.in/~rbahadur/affinity.odt)**

**Table 1: The benchmark dataset for the protein-RNA binding
affinity.**

|  |  |  |  |  |  |  |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| PDB IDa  Complex | Protein | RNA | Length of the RNA | | Kd (M) | Temp (K) | pH | ΔGb (kcal/mol) | Expc | Interface Area (B) (Å2)d | c-rmsde (Å) | i-rmsdf(Å) | Reference |
| Crystal | Solution |
| A. Complexes with tRNA (5) | | | | | | | | | | | | | |
| [1asy (A:R)](http://www.rcsb.org/pdb/explore/explore.do?structureId=1ASY) | Aspartyl-tRNA synthetase | tRNA (Asp) | 75 | 76 | 3.0x10-8 | 310 | 5.5 | 10.66 | A | 4430 | 1.5 | 1.3  *2.3* | [(1)](http://www.ncbi.nlm.nih.gov/pubmed/10452887) |
| [1qtq (A:B)](http://www.rcsb.org/pdb/explore/explore.do?structureId=1QTQ) | Glutaminyl-tRNA synthetase | tRNA (Gln) | 75 | 76 | 3.6x10-7 | 310 | 5.2 | 9.13 | D | 5200 | 1.6 | 1.8 | [(2)](http://www.ncbi.nlm.nih.gov/pubmed/15845537) |
| [1u0b](http://www.rcsb.org/pdb/explore/explore.do?structureId=1U0B)  (B:A) | Cysteinyl-tRNA synthetase | tRNA (Cys) | 74 | 74 | 2.7x10-7 | 298 | 7.5 | 8.95 | B | 4560 | 0.7 | 1.0 | [(3)](http://www.ncbi.nlm.nih.gov/pubmed/15489861) |
| [2drb](http://www.rcsb.org/pdb/explore/explore.do?structureId=2DRB) (A:B) | CCA-adding enzyme | tRNA (35-mer) | 35 | 73 | 6.7 x10-8 | 298 | 8.5 | 9.78 | C | 3200 | 1.1 | 1.8 | [(4)](http://www.ncbi.nlm.nih.gov/pubmed/14592988) |
| [2fmt](http://www.rcsb.org/pdb/explore/explore.do?structureId=2FMT) (A:C) | tRNA-fMettransformylase | tRNA (fMet) | 77 | 77 | 1.36x10-7 | 310 | 7.6 | 9.73 | A | 2940 | 1.2 | 0.9  *1.7* | [(5)](http://www.ncbi.nlm.nih.gov/pubmed/2190631) |
| B. Ribosomal protein (2) | | | | | | | | | | | | | |
| [1dfu (P:MN)](http://www.rcsb.org/pdb/explore/explore.do?structureId=1DFU) | Ribosomal protein L25 | 5S rRNA | 19 | 120 | 6.7x10-8 | 298 | 7.6 | 9.78 | A | 1690 | 3.0 | 3.0  *3.7* | [(6)](http://www.ncbi.nlm.nih.gov/pubmed/365228) |
| [1sds](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SDS) (C:FF′) | Ribosomal protein L7Ae | box H/ACA sRNA | 15 | 84 | 7.5x10-8 | 277 | 7.4 | 9.03 | C | 1200 | 0.3 | 0.4 | [(7)](http://www.ncbi.nlm.nih.gov/pubmed/12560482) |
| C. Duplex RNA (2) | | | | | | | | | | | | | |
| [1yvpg](http://www.rcsb.org/pdb/explore/explore.do?structureId=1YVP) (B:EFH) | Ro autoantigen | Y RNA | 10 | 97 | 5.2x10-9 | 277 | 7.5 | 10.49 | C | 3500 | 1.4 | 1.3 | [(8)](http://www.ncbi.nlm.nih.gov/pubmed/15907467) |
| [2az0](http://www.rcsb.org/pdb/explore/explore.do?structureId=2AZ0) (AB:CD) | Silencing suppressor protein B2 | siRNA | 18 | 19 | 1.4x10-9 | 277 | 7.5 | 11.22 | C | 1970 | 1.3 | 1.0 | [(9)](http://www.ncbi.nlm.nih.gov/pubmed/16228003) |
| D. Single stranded RNA (6) | | | | | | | | | | | | | |
| [1jbs (A:C)](http://www.rcsb.org/pdb/explore/explore.do?structureId=1JBS) | Sarcin-like cytotoxin restrictocin | 29-mer SRD RNA analog | 29 | 29 | 1.0x10-6 | 298 | 7.2 | 8.18 | B | 1310 | 0.7 | 0.6  *1.9* | [(10)](http://www.ncbi.nlm.nih.gov/pubmed/11685244) |
| [1wsu](http://www.rcsb.org/pdb/explore/explore.do?structureId=1WSU) (A:E) | Elongation factor SelB | SECIS RNA | 23 | 23 | 1.0x10-6 | 277 | 5.4 | 7.60 | C | 940 | 0.7 | 0.5  *0.8* | [(11)](http://www.ncbi.nlm.nih.gov/pubmed/15665870) |
| [2a8v](http://www.rcsb.org/pdb/explore/explore.do?structureId=2A8V) (B:E) | Rho transcription termination factor | Cytosine-rich RNA | 6 | 10 | 5.0x10-6 | 298 | 8.0 | 7.22 | A | 720 | 1.0 | 1.6 | [(12)](http://www.ncbi.nlm.nih.gov/pubmed/8632473) |
| [2asb](http://www.rcsb.org/pdb/explore/explore.do?structureId=2ASB) (A:B) | NusA antiterminator | BoxC rRNA | 11 | 13 | 1.15x10-7 | 291 | 7.8 | 9.23 | E | 2320 | 1.1 | 0.8 | [(13)](http://www.ncbi.nlm.nih.gov/pubmed/16193062) |
| [2b6g](http://www.rcsb.org/pdb/explore/explore.do?structureId=2B6G) (A:B) | Vts1p | SRE hairpin RNA | 19 | 15 | 1.7x10-8 | 277 | 7.0 | 9.84 | B | 483 | 0.9 | 0.3  *0.9* | [(14)](http://www.ncbi.nlm.nih.gov/pubmed/12858164) |
| [2ix1](http://www.rcsb.org/pdb/explore/explore.do?structureId=2IX1) (A:B) | RNase II | Single-stranded RNA | 13 | 25 | 5.3x10-9 | 277 | 8.0 | 10.48 | F | 4160 | 1.6 | 0.9 | [(15)](http://www.ncbi.nlm.nih.gov/pubmed/18337246) |

 

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. Symmetry-related chains are primed (e.g., FF′ in
1sds).

bGibbs free energy
calculated from ΔG= -RT lnKd, where R is the gas constant and T is the
absolute temperature.

cExperimental
methods used for the determination of Kd: (A) Filtration assay; (B)
Fluorescence titration; (C) Electrophoretic mobility shift assay; (D) Binding
kinetics; (E) Isothermal titration calorimetry; (F)
Surface plasma resonance

dData taken from
Barik et al. [(16).](http://www.ncbi.nlm.nih.gov/pubmed/22488669)

ec-rmsd is
calculated over all the Cα atoms of a given protein chain. Data
are taken from Barik et al [(16).](http://www.ncbi.nlm.nih.gov/pubmed/22488669)

fi-rmsd
is calculated considering only the interface Cα atoms, and the
values in italics include the phosphorus atoms of the interface nucleotides
when the corresponding RNA structure is available in the unbound form. Data are
taken from Barik et al [(16).](http://www.ncbi.nlm.nih.gov/pubmed/22488669)

gDissociation constant represents the duplex strand
of the Y RNA involving E and F chains.

**References**

1. Eriani, G. and Gangloff, J. (1999)
Yeast aspartyl-tRNA synthetase residues interacting with tRNA(Asp) identity bases connectively contribute to tRNA(Asp) binding in the ground and transition-state complex and discriminate against non-cognate tRNAs. *J Mol Biol*, **291**, 761-773.

2. Uter, N.T., Gruic-Sovulj, I. and
Perona, J.J. (2005) Amino acid-dependent transfer RNA affinity in a class I
aminoacyl-tRNA synthetase. *J Biol Chem*,
**280**, 23966-23977.

3. Hauenstein, S., Zhang, C.M., Hou, Y.M.
and Perona, J.J. (2004) Shape-selective RNA recognition by cysteinyl-tRNA
synthetase. *Nat Struct Mol Biol*, **11**, 1134-1141.

4. Okabe, M., Tomita, K., Ishitani, R.,
Ishii, R., Takeuchi, N., Arisaka, F., Nureki, O. and Yokoyama, S. (2003)
Divergent evolutions of trinucleotide polymerization revealed by an archaeal
CCA-adding enzyme structure. *EMBO J*, **22**, 5918-5927.

5. Janiak, F., Dell, V.A., Abrahamson,
J.K., Watson, B.S., Miller, D.L. and Johnson, A.E. (1990) Fluorescence
characterization of the interaction of various transfer RNA species with
elongation factor Tu.GTP: evidence for a new functional role for elongation
factor Tu in protein biosynthesis. *Biochemistry*,
**29**, 4268-4277.

6. Spierer, P., Bogdanov, A.A. and Zimmermann,
R.A. (1978) Parameters for the interaction of ribosomal proteins L5, L18, and
L25 with 5S RNA from Escherichia coli. *Biochemistry*,
**17**, 5394-5398.

7. Rozhdestvensky, T.S., Tang, T.H.,
Tchirkova, I.V., Brosius, J., Bachellerie, J.P. and Huttenhofer, A. (2003)
Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding
motif for C/D and H/ACA box snoRNAs in Archaea. *Nucleic Acids Res*, **31**,
869-877.

8. Stein, A.J., Fuchs, G., Fu, C., Wolin,
S.L. and Reinisch, K.M. (2005) Structural insights into RNA quality control:
the Ro autoantigen binds misfolded RNAs via its central cavity. *Cell*, **121**, 529-539.

9. Chao, J.A., Lee, J.H., Chapados, B.R.,
Debler, E.W., Schneemann, A. and Williamson, J.R. (2005) Dual modes of
RNA-silencing suppression by Flock House virus protein B2. *Nat Struct Mol Biol*, **12**,
952-957.

10. Yang, X., Gerczei, T., Glover, L.T. and
Correll, C.C. (2001) Crystal structures of restrictocin-inhibitor complexes
with implications for RNA recognition and base flipping. *Nat Struct Biol*, **8**,
968-973.

11. Yoshizawa, S., Rasubala, L., Ose, T.,
Kohda, D., Fourmy, D. and Maenaka, K. (2005) Structural basis for mRNA
recognition by elongation factor SelB. *Nat
Struct Mol Biol*, **12**, 198-203.

12. Martinez, A., Opperman, T. and
Richardson, J.P. (1996) Mutational analysis and secondary structure model of
the RNP1-like sequence motif of transcription termination factor Rho. *J Mol Biol*, **257**, 895-908.

13. Beuth, B., Pennell, S., Arnvig, K.B.,
Martin, S.R. and Taylor, I.A. (2005) Structure of a Mycobacterium tuberculosis
NusA-RNA complex. *EMBO J*, **24**, 3576-3587.

14. Aviv, T., Lin, Z., Lau, S., Rendl, L.M.,
Sicheri, F. and Smibert, C.A. (2003) The RNA-binding SAM domain of Smaug
defines a new family of post-transcriptional regulators. *Nat Struct Biol*, **10**,
614-621.

15. Barbas, A., Matos, R.G., Amblar, M.,
Lopez-Vinas, E., Gomez-Puertas, P. and Arraiano, C.M. (2008) New insights into
the mechanism of RNA degradation by ribonuclease II: identification of the
residue responsible for setting the RNase II end product. *J Biol Chem*, **283**,
13070-13076.

16. Barik, A., Nithin, C., Manasa, P. and
Bahadur, R.P. (2012) A protein-RNA docking benchmark (I): nonredundant cases. *Proteins*, **80**, 1866-1871.