1EJO

FAB FRAGMENT OF NEUTRALISING MONOCLONAL ANTIBODY 4C4 COMPLEXED WITH G-H LOOP FROM FMDV.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A multiply substituted G-H loop from foot-and-mouth disease virus in complex with a neutralizing antibody: a role for water molecules.

Ochoa, W.F.Kalko, S.G.Mateu, M.G.Gomes, P.Andreu, D.Domingo, E.Fita, I.Verdaguer, N.

(2000) J Gen Virol 81: 1495-1505

  • DOI: 10.1099/0022-1317-81-6-1495
  • Primary Citation of Related Structures:  
    1EJO

  • PubMed Abstract: 
  • The crystal structure of a 15 amino acid synthetic peptide, corresponding to the sequence of the major antigenic site A (G-H loop of VP1) from a multiple variant of foot-and-mouth disease virus (FMDV), has been determined at 2.3 A resolution. The var ...

    The crystal structure of a 15 amino acid synthetic peptide, corresponding to the sequence of the major antigenic site A (G-H loop of VP1) from a multiple variant of foot-and-mouth disease virus (FMDV), has been determined at 2.3 A resolution. The variant peptide includes four amino acid substitutions in the loop relative to the previously studied peptide representing FMDV C-S8c1 and corresponds to the loop of a natural FMDV isolate of subtype C(1). The peptide was complexed with the Fab fragment of the neutralizing monoclonal antibody 4C4. The peptide adopts a compact fold with a nearly cyclic conformation and a disposition of the receptor-recognition motif Arg-Gly-Asp that is closely related to the previously determined structure for the viral loop, as part of the virion, and for unsubstituted synthetic peptide antigen bound to neutralizing antibodies. New structural findings include the observation that well-defined solvent molecules appear to play a major role in stabilizing the conformation of the peptide and its interactions with the antibody. Structural results are supported by molecular-dynamic simulations. The multiply substituted peptide developed compensatory mechanisms to bind the antibody with a conformation very similar to that of its unsubstituted counterpart. One water molecule, which for steric reasons could not occupy the same position in the unsubstituted antigen, establishes hydrogen bonds with three peptide amino acids. The constancy of the structure of an antigenic domain despite multiple amino acid substitutions has implications for vaccine design.


    Organizational Affiliation

    Instituto Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi-Girona 18-26, 08034 Barcelona, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A MONOCLONAL ANTIBODY (LIGHT CHAIN)L216Mus musculusMutation(s): 0 
Find proteins for P01660 (Mus musculus)
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Go to UniProtKB:  P01660
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A MONOCLONAL ANTIBODY (HEAVY CHAIN)H220Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q6PF95 (Mus musculus)
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Go to UniProtKB:  Q6PF95
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FMDV PEPTIDEP15N/AMutation(s): 0 
Find proteins for P15072 (Foot-and-mouth disease virus (isolate -/Germany/C1Oberbayen/1960 serotype C))
Explore P15072 
Go to UniProtKB:  P15072
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.18α = 90
b = 69.328β = 90
c = 146.539γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation