CSB Lab

Protein-RNA affinity Benchmark

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

PDB ID^a Complex	Protein	RNA	Length of the RNA		K_d (M)	Temp (K)	pH	ΔG^b (kcal/mol)	Exp^c	Interface Area (B) (Å²)^d	c-rmsd^e (Å)	i-rmsd^f(Å)	Reference
PDB ID^a Complex	Protein	RNA	Crystal	Solution	K_d (M)	Temp (K)	pH	ΔG^b (kcal/mol)	Exp^c	Interface Area (B) (Å²)^d	c-rmsd^e (Å)	i-rmsd^f(Å)	Reference
A. Complexes with tRNA (5)
1asy (A:R)	Aspartyl-tRNA synthetase	tRNA (Asp)	75	76	3.0x10^-8	310	5.5	10.66	A	4430	1.5	1.3 2.3	(1)
1qtq (A:B)	Glutaminyl-tRNA synthetase	tRNA (Gln)	75	76	3.6x10^-7	310	5.2	9.13	D	5200	1.6	1.8	(2)
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)
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)
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)
B. Ribosomal protein (2)
1dfu (P:MN)	Ribosomal protein L25	5S rRNA	19	120	6.7x10^-8	298	7.6	9.78	A	1690	3.0	3.0 3.7	(6)
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)
C. Duplex RNA (2)
1yvp^g (B:EFH)	Ro autoantigen	Y RNA	10	97	5.2x10^-9	277	7.5	10.49	C	3500	1.4	1.3	(8)
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)
D. Single stranded RNA (6)
1jbs (A:C)	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)
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)
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)
2asb (A:B)	NusA antiterminator	BoxC rRNA	11	13	1.15x10^-7	291	7.8	9.23	E	2320	1.1	0.8	(13)
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)
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)

^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 lnK_d, where R is the gas constant and T is the absolute temperature.

^cExperimental methods used for the determination of K_d: (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).

^ec-rmsd is calculated over all the C_αatoms of a given protein chain. Data are taken from Barik et al (16).

^fi-rmsd is calculated considering only the interface C_αatoms, 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).

^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.