PDBsum entry 5mjv

Virus

PDB id: 5mjv

Contents

Protein chains

192 a.a.

239 a.a.

257 a.a.

DNA/RNA

PDB id:

5mjv

Name:

Virus

Title:

Rebuild and re-refined model for human parechovirus 1

Structure:

Capsid subunit vp1. Chain: a. Engineered: yes. Capsid subunit vp3. Chain: b. Engineered: yes. Capsid subunit vp0. Chain: c. Engineered: yes.

Source:

Human parechovirus 1 (strain harris). Hpev-1. Organism_taxid: 103911. Strain: harris. Atcc: vr-52. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: a549. Expression_system_atcc_number: ccl-185.

Resolution:

3.09Å R-factor: 0.258 R-free: 0.261

Authors:

S.Shakeel,E.C.Dykeman,S.J.White,A.Ora,J.J.B.Cockburn,S.J.Butcher, P.G.Stockley,R.Twarock

Key ref:

S.Shakeel et al. (2017). Genomic RNA folding mediates assembly of human parechovirus. Nat Commun, 8, 5. PubMed id: 28232749 DOI: 10.1038/s41467-016-0011-z

Date:

01-Dec-16 Release date: 11-Jan-17

Supersedes:

5m74

Protein chain

Q66578  (POLG_HPE1H) -  Genome polyprotein from Human parechovirus 1 (strain Harris)

Seq: 2180 a.a.

Struc: 192 a.a.

Protein chain

Q66578  (POLG_HPE1H) -  Genome polyprotein from Human parechovirus 1 (strain Harris)

Seq: 2180 a.a.

Struc: 239 a.a.

Protein chain

Q66578  (POLG_HPE1H) -  Genome polyprotein from Human parechovirus 1 (strain Harris)

Seq: 2180 a.a.

Struc: 257 a.a.

DNA/RNA chain

G-U-U-U-U-U 6 bases

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.3.6.1.15 - 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: 10.1038/s41467-016-0011-z

Nat Commun 8:5 (2017)

PubMed id: 28232749

Genomic RNA folding mediates assembly of human parechovirus.

S.Shakeel, E.C.Dykeman, S.J.White, A.Ora, J.J.Cockburn, S.J.Butcher, P.G.Stockley, R.Twarock.

ABSTRACT

Assembly of the major viral pathogens of the Picornaviridae family is poorly understood. Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. We show here via a combination of RNA-based systematic evolution of ligands by exponential enrichment, bioinformatics analysis and reverse genetics that these RNA segments are bound to the coat proteins in a sequence-specific manner. Disruption of either the RNA coat protein recognition motif or its contact amino acid residues is deleterious for viral assembly. The data are consistent with RNA packaging signals playing essential roles in virion assembly. Their binding sites on the coat proteins are evolutionarily conserved across the Parechovirus genus, suggesting that they represent potential broad-spectrum anti-viral targets.The mechanism underlying packaging of genomic RNA into viral particles is not well understood for human parechoviruses. Here the authors identify short RNA motifs in the parechovirus genome that bind capsid proteins, providing approximately 60 specific interactions for virion assembly.