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: 2.10 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 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

  • Structures With Same Primary Citation

  • 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: 
    • 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
    • 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

    Organizational Affiliation

    Institute of Biochemistry, University of Vienna, Austria.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS CAPSID PROTEIN VP2P16Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A 8F5 FAB (LIGHT CHAIN)L220Mus musculusMutation(s): 0 
Gene Names: Igkv8-30Gm10883
Find proteins for Q52L64 (Mus musculus)
Explore Q52L64 
Go to UniProtKB:  Q52L64
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A 8F5 FAB (HEAVY CHAIN)H218Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q505N9 (Mus musculus)
Explore Q505N9 
Go to UniProtKB:  Q505N9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.79α = 90
b = 76.32β = 90
c = 92.32γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
AGROVATAdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATA)data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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