PDBsum entry 1msc

Viral protein

PDB id: 1msc

Contents

Protein chain

129 a.a. *

Waters ×111

* Residue conservation analysis

PDB id:

1msc

Name:

Viral protein

Title:

Crystal structure of ms2 coat protein dimer

Structure:

Bacteriophage ms2 coat protein. Chain: a. Engineered: yes

Source:

Enterobacterio phage ms2. Organism_taxid: 12022. Gene: ms2 coat gene. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.200

Authors:

C.-Z.Ni,R.Kodandapani,K.R.Ely

Key ref:

C.Z.Ni et al. (1995). Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly. Structure, 3, 255-263. PubMed id: 7788292 DOI: 10.1016/S0969-2126(01)00156-3

Date:

28-Apr-95 Release date: 10-Jul-95

Protein chain

P03612  (CAPSD_BPMS2) -  Capsid protein from Escherichia phage MS2

Seq: 130 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(01)00156-3

Structure 3:255-263 (1995)

PubMed id: 7788292

Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly.

C.Z.Ni, R.Syed, R.Kodandapani, J.Wickersham, D.S.Peabody, K.R.Ely.

ABSTRACT

BACKGROUND: The coat protein in RNA bacteriophages binds and encapsidates viral RNA, and also acts as translational repressor of viral replicase by binding to an RNA hairpin in the RNA genome. Because of its dual function, the MS2 coat protein is an interesting candidate for structural studies of protein-RNA interactions and protein-protein interactions. In this study, unassembled MS2 coat protein dimers were selected to analyze repressor activity and virus assembly. RESULTS: The crystal structure of a mutant MS2 coat protein that is defective in viral assembly yet retains repressor activity has been determined at 2.0 A resolution. The unassembled dimer is stabilized by interdigitation of alpha-helices, and the formation of a 10-stranded antiparallel beta-sheet across the interface between monomers. The substitution of arginine for tryptophan at residue 82 results in the formation of two new inter-subunit hydrogen bonds that further stabilize the dimer. Residues that influence RNA recognition, identified by molecular genetics, were located across the beta-sheet. Two of these residues (Tyr85 and Asn87) are displaced in the unliganded dimer and are located in the same beta-strand as the Trp-->Arg mutation. CONCLUSIONS: When compared with the structure of the coat protein in the assembled virus, differences in orientation of residues 85 and 87 suggest conformational adjustment on binding RNA in the first step of viral assembly. The substitution at residue 82 may affect virus assembly by imposing conformational restriction on the loop that makes critical inter-subunit contacts in the capsid.

Selected figure(s)

Figure 3.
Figure 3. Electron-density map in the region of the interface between monomeric subunits in the repressor dimer. Contours from the 2F[o]–F[c] electron-density map (2 å resolution) are drawn at the 1.5σ level and shown with blue lines. The model of one monomer is shown in green in the contour map, with the other monomer in red. At this interface the two β-strands G (residues 82–94) are arranged in an antiparallel fashion with extensive hydrogen-bonded interactions between the two monomers. Figure 3. Electron-density map in the region of the interface between monomeric subunits in the repressor dimer. Contours from the 2F[o]–F[c] electron-density map (2 å resolution) are drawn at the 1.5σ level and shown with blue lines. The model of one monomer is shown in green in the contour map, with the other monomer in red. At this interface the two β-strands G (residues 82–94) are arranged in an antiparallel fashion with extensive hydrogen-bonded interactions between the two monomers.

Figure 7.
Figure 7. View comparing the atomic models of amino acid residues near Phe95 in the unassembled dimer (blue) and viral subunit C-C′ (red). The image has been ‘clipped’ for clarity. The Phe95 ring in the isolated dimer has moved vert, similar 7 å relative to the position in the viral capsid and this conformational change is a result of the Trp82→Arg substitution. The guanidinium group of Arg82 from the opposite subunit in the dimer is accommodated by this rotation of the Phe95 side chain. Note that without this conformational change there would be a severe steric clash of these two residues. Figure 7. View comparing the atomic models of amino acid residues near Phe95 in the unassembled dimer (blue) and viral subunit C-C′ (red). The image has been ‘clipped’ for clarity. The Phe95 ring in the isolated dimer has moved [3]not, vert, similar 7 å relative to the position in the viral capsid and this conformational change is a result of the Trp82→Arg substitution. The guanidinium group of Arg82 from the opposite subunit in the dimer is accommodated by this rotation of the Phe95 side chain. Note that without this conformational change there would be a severe steric clash of these two residues.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 255-263) copyright 1995.

Figures were selected by an automated process.