PDBsum entry 1a3r

Viral protein/immune system

PDB id: 1a3r

Contents

Protein chains

220 a.a. *

212 a.a. *

16 a.a. *

Waters ×213

* Residue conservation analysis

PDB id:

1a3r

Name:

Viral protein/immune system

Title:

Fab fragment (antibody 8f5) complexed with peptide from human rhinovirus (serotype 2) viral capsid protein vp2 (residues 156-170)

Structure:

Igg2a 8f5 fab (light chain). Chain: l. Fragment: fab fragment (papain digestion). Synonym: antibody 8f5. Igg2a 8f5 fab (heavy chain). Chain: h. Fragment: fab fragment (papain digestion). Synonym: antibody 8f5. Human rhinovirus capsid protein vp2.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2. Other_details: common cold virus

Biol. unit:

Trimer (from PQS)

Resolution:

2.10Å R-factor: 0.171

Authors:

J.Tormo,D.Blaas,I.Fita

Key ref:

J.Tormo et al. (1994). Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. Embo J, 13, 2247-2256. PubMed id: 8194515

Date:

23-Jan-98 Release date: 29-Apr-98

Protein chain

Q52L64  (Q52L64_MOUSE) -  ENSMUSG00000076577 protein from Mus musculus

Seq: 240 a.a.

Struc: 220 a.a.*

Protein chain

Q505N9  (Q505N9_MOUSE) -  Igh protein from Mus musculus

Seq: 468 a.a.

Struc: 212 a.a.*

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 16 a.a.*

* PDB and UniProt seqs differ at 44 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain P: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chain P: 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: Chain P: 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: Chain P: 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

Embo J 13:2247-2256 (1994)

PubMed id: 8194515

Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2.

J.Tormo, D.Blaas, N.R.Parry, D.Rowlands, D.Stuart, I.Fita.

ABSTRACT

The three-dimensional structure of the complex between the Fab fragment of an anti-human rhinovirus neutralizing antibody (8F5) and a cross-reactive synthetic peptide from the viral capsid protein VP2 has been determined at 2.5 A resolution by crystallographic methods. The refinement is presently at an R factor of 0.18 and the antigen-binding site and viral peptide are well defined. The peptide antigen adopts a compact fold by two tight turns and interacts through hydrogen bonds, some with ionic character, and van der Waals contacts with antibody residues from the six hypervariable loops as well as several framework amino acids. The conformation adopted by the peptide is closely related to the corresponding region of the viral protein VP2 on the surface of human rhinovirus 1A whose three-dimensional structure is known. Implications for the cross-reactivity between peptides and the viral capsid are discussed. The peptide-antibody interactions, together with the analysis of mutant viruses that escape neutralization by 8F5 suggest two different mechanisms for viral escape. The comparison between the complexed and uncomplexed antibody structures shows important conformational rearrangements, especially in the hypervariable loops of the heavy chain. Thus, it constitutes a clear example of the 'induced fit' molecular recognition mechanism.