PDBsum entry 3iyc

Viral protein

PDB id: 3iyc

Contents

Protein chains

235 a.a.*

14 a.a.*

231 a.a.* *

232 a.a.* *

11 a.a.* *

* Residue conservation analysis

* C-alpha coords only

PDB id:

3iyc

Name:

Viral protein

Title:

Poliovirus late RNA-release intermediate

Structure:

Capsid protein vp1. Chain: 1. Synonym: p1d,virion protein 1. Engineered: yes. Capsid protein vp2. Chain: 2. Synonym: p1b,virion protein 2. Engineered: yes. Genome polyprotein.

Source:

Human poliovirus 1 mahoney. Organism_taxid: 12081. Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b). Organism_taxid: 12088. Poliovirus 1. Organism_taxid: 12080. Human poliovirus 1. Organism_taxid: 12080

Authors:

H.C.Levy,M.Bostina,D.J.Filman,J.M.Hogle

Key ref:

H.C.Levy et al. (2010). Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. J Virol, 84, 4426-4441. PubMed id: 20181687

Date:

21-Jul-09 Release date: 16-Mar-10

Protein chain

P03300  (POLG_POL1M) -  Genome polyprotein from Poliovirus type 1 (strain Mahoney)

Seq: 2209 a.a.

Struc: 235 a.a.

Protein chain

P03302  (POLG_POL3L) -  Genome polyprotein from Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)

Seq: 2206 a.a.

Struc: 14 a.a.

Protein chain

Q9E8Z2  (Q9E8Z2_9ENTO) -  Genome polyprotein from Poliovirus 1

Seq: 2209 a.a.

Struc: 231 a.a.

Protein chain

P03300  (POLG_POL1M) -  Genome polyprotein from Poliovirus type 1 (strain Mahoney)

Seq: 2209 a.a.

Struc: 232 a.a.

Protein chain

No UniProt id for this chain

Struc: 11 a.a.

Enzyme reactions

• Enzyme class 2: Chains 1, 2, 3, 4: 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 1, 2, 3, 4: 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 1, 2, 3, 4: 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 1, 2, 3, 4: 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

J Virol 84:4426-4441 (2010)

PubMed id: 20181687

Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.

H.C.Levy, M.Bostina, D.J.Filman, J.M.Hogle.

ABSTRACT

Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes associated with the release of the RNA genome, we have used cryo-electron microscopy to characterize the structure of the 80S "empty" particles of poliovirus that are thought to represent the final product of the cell entry pathway. Using two-dimensional classification methods, we show that preparations of 80S particles contain at least two structures, which might represent snapshots from a continuous series of conformers. Using three-dimensional reconstruction methods, we have solved the structure of two distinct forms at subnanometric resolution, and we have built and refined pseudoatomic models into the reconstructions. The reconstructions and the derived models demonstrate that the two structural forms are both slightly expanded, resulting in partial disruption of interprotomer interfaces near their particle 2-fold axes, which may represent the site where RNA is released. The models demonstrate that each of the two 80S structures has undergone a unique set of movements of the capsid proteins, associated with rearrangement of flexible loops and amino-terminal extensions that participate in contacts between protomers, between pentamers, and with the viral RNA.