PDBsum entry 4l3b

Virus

PDB id: 4l3b

Contents

Protein chains

222 a.a.

248 a.a.

237 a.a.

PDB id:

4l3b

Name:

Virus

Title:

X-ray structure of the hrv2 a particle uncoating intermediate

Structure:

Protein vp1. Chain: a. Fragment: unp residues 568-856. Synonym: p1d, virion protein 1. Protein vp2. Chain: b. Fragment: unp residues 70-330. Synonym: p1b, virion protein 2. Protein vp3.

Source:

Human rhinovirus a2. Hrv-2. Organism_taxid: 12130. Organism_taxid: 12130

Resolution:

6.50Å R-factor: 0.309 R-free: 0.320

Authors:

L.Vives-Adrian,J.Querol-Audi,D.Garriga,J.Pous,N.Verdaguer

Key ref:

A.Pickl-Herk et al. (2013). Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Proc Natl Acad Sci U S A, 110, 20063-20068. PubMed id: 24277846 DOI: 10.1073/pnas.1312128110

Date:

05-Jun-13 Release date: 27-Nov-13

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 222 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 248 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 237 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: Chains A, B, C: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: Chains A, B, C: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1312128110

Proc Natl Acad Sci U S A 110:20063-20068 (2013)

PubMed id: 24277846

Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.

A.Pickl-Herk, D.Luque, L.Vives-Adrián, J.Querol-Audí, D.Garriga, B.L.Trus, N.Verdaguer, D.Blaas, J.R.Castón.

ABSTRACT

During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.