1A3R

FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(1994) EMBO J. 13: 2247-2256


  • PubMed 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 crysta ...

    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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Fab Fragment of a Neutralizing Monoclonal Antibody Directed Against Human Rhinovirus Serotype 2
      Tormo, J.,Fita, I.,Kanzler, O.,Blaas, D.
      (1990) J.Biol.Chem. 265: 16799
    • Three-Dimensional Structure of the Fab Fragment of a Neutralizing Antibody to Human Rhinovirus Serotype 2
      Tormo, J.,Stadler, E.,Skern, T.,Auer, H.,Kanzler, O.,Betzel, C.,Blaas, D.,Fita, I.
      (1992) Protein Sci. 1: 1154


    Organizational Affiliation

    Institute of Biochemistry, University of Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A 8F5 FAB (LIGHT CHAIN)
L
220Mus musculusMutation(s): 0 
Gene Names: Igkv8-30 (Gm10883)
Find proteins for Q52L64 (Mus musculus)
Go to UniProtKB:  Q52L64
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A 8F5 FAB (HEAVY CHAIN)
H
218Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q505N9 (Mus musculus)
Go to UniProtKB:  Q505N9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS CAPSID PROTEIN VP2
P
16Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P
NON-POLYMERH2 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.790α = 90.00
b = 76.320β = 90.00
c = 92.320γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
CCP4data scaling
AGROVATAdata reduction
ROTAVATAdata reduction
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
ROTAVATA)data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance