1EJO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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

  • 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 BiologĂ­a Molecular de Barcelona, Consejo Superior de Investigaciones CientĂ­ficas, Jordi-Girona 18-26, 08034 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A MONOCLONAL ANTIBODY (LIGHT CHAIN)
L
216Mus musculusN/A
Find proteins for P01660 (Mus musculus)
Go to UniProtKB:  P01660
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A MONOCLONAL ANTIBODY (HEAVY CHAIN)
H
220Mus musculusGene Names: Igh
Find proteins for Q6PF95 (Mus musculus)
Go to UniProtKB:  Q6PF95
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FMDV PEPTIDE
P
15Foot-and-mouth disease virusEC: 3.4.22.46
Find proteins for P15072 (Foot-and-mouth disease virus)
Go to UniProtKB:  P15072
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.180α = 90.00
b = 69.328β = 90.00
c = 146.539γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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