PDBsum entry: 2voo

RNA-binding protein

PDB id: 2voo

Contents

Protein chains

179 a.a. *

DNA/RNA

Waters ×201

* Residue conservation analysis

PDB id:

2voo

Name:

RNA-binding protein

Title:

Crystal structure of n-terminal domains of human la protein complexed with RNA oligomer uuuuuuuu

Structure:

Lupus la protein. Chain: a, b. Fragment: n-terminal domain, residues 4-194. Synonym: human la protein, sjoegren syndrome type b antigen, ss-b, la ribonucleoprotein, la autoantigen. Engineered: yes. 5'-r( Up Up Up Up Up Up Up)-3'. Chain: c, d

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.80Å R-factor: 0.250 R-free: 0.279

Authors:

O.Kotik-Kogan,E.R.Valentine,D.Sanfelice,M.R.Conte,S.Curry

Key ref:

O.Kotik-Kogan et al. (2008). Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein. Structure, 16, 852-862. PubMed id: 18547518 DOI: 10.1016/j.str.2008.02.021

Date:

19-Feb-08 Release date: 06-May-08

Protein chains

P05455  (LA_HUMAN) -  Lupus La protein

Seq: 408 a.a.

Struc: 179 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonucleoprotein complex (2 terms)
• Biological process: RNA processing (1 term)
• Biochemical function: nucleotide binding (3 terms)

DOI no: 10.1016/j.str.2008.02.021

Structure 16:852-862 (2008)

PubMed id: 18547518

Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein.

O.Kotik-Kogan, E.R.Valentine, D.Sanfelice, M.R.Conte, S.Curry.

ABSTRACT

The eukaryotic La protein recognizes the 3' poly(U) sequences of nascent RNA polymerase III transcripts to assist folding and maturation. The 3' ends of such RNAs are bound by the N-terminal domain of La (LaNTD). We have solved the crystal structures of four LaNTD:RNA complexes, each containing a different single-stranded RNA oligomer, and compared them to the structure of a previously published LaNTD:RNA complex containing partially duplex RNA. The presence of purely single-stranded RNA in the binding pocket at the interface between the La motif and RRM domains allows significantly closer contact with the 3' end of the RNA. Comparison of the different LaNTD:RNA complexes identifies a conserved set of interactions with the last two nucleotides at the 3' end of the RNA ligand that are key to binding. Strikingly, we also observe two alternative conformations of bound ssRNA, indicative of an unexpected degree of plasticity in the modes of RNA binding.

Selected figure(s)

Figure 1.
Figure 1. Structure and Comparison of LaNTD:RNA Complexes
(A) Simulated annealing F[o] − F[c] omit map contoured at 1.75σ showing density for the AUAAUUU RNA oligomer bound to LaNTD. The protein is colored by domain: La motif, orange; interdomain linker, green; RRM1, brown. All structural figures were prepared using PyMOL (DeLano, 2002).
(B) Comparison of LaNTD complexes with ssRNA and dsRNA, superposed using residues of the La motif. Top: the superposition of LaNTD complexes with the ssRNAs AUUUU (pink), AUAAUUU (green), and UUUUUUUU (brown) reveals a high degree of similarity. Bottom: superposition of LaNTD complexed with AUUUU (pink) and the self-annealing duplex RNA UGCUGUUUU (blue) reveals that the dsRNA ligand displaces RRM1 away from the La motif, increasing the width of the interdomain cleft.
(C) Superposition of LaNTD:RNA complexes showing variation in the conformations of bound RNA. The protein is colored as in (A). The RNA oligomers shown are AUUUU (magenta), AUAAUUU (green), UUUUUUUU (orange), and the duplex of UGCUGUUUU (blue). Note that only the last two U's of UUUUUUUU are included in the model.

Figure 4.
Figure 4. Gel-Shift Analysis of LaNTD:RNA Interactions
(A) Autoradiograms of the gel analysis of radiolabeled RNA oligomers. Details are given in Experimental Procedures. Protein concentration is shown on the top and the RNA oligomer used in each experiment is indicated within each panel.
(B) Sample fits of the binding data are shown for CACACAUUUU, CACACAAUUU, CACACAUAUU, and CACACAAAUU. Binding curves are shown for selected RNA oligomers.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 852-862) copyright 2008.

Figures were selected by an automated process.