3EYQ

Crystal structure of MJ5 Fab, a germline antibody variant of anti-human cytomegalovirus antibody 8f9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus.

Thomson, C.A.Bryson, S.McLean, G.R.Creagh, A.L.Pai, E.F.Schrader, J.W.

(2008) Embo J. 27: 2592-2602

  • DOI: 10.1038/emboj.2008.179
  • Primary Citation of Related Structures:  3EYF, 3EYO, 3F12

  • PubMed Abstract: 
  • Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are un ...

    Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are under positive evolutionary selection, raising the possibility that V-genes have been selected to encode key structural features of binding sites of protective antibodies against certain pathogens. Human, neutralizing antibodies to human cytomegalovirus that bind the AD-2S1 epitope on its gB envelope protein repeatedly use a pair of well-conserved, germline V-genes IGHV3-30 and IGKV3-11. Here, we present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hypermutated, high-affinity neutralizing antibody. V-genes may thus encode an innate, protective immunological memory that targets vulnerable, invariant sites on multiple pathogens.


    Organizational Affiliation

    The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M2J5 Fab
C
216Homo sapiensGene Names: IGK@
Find proteins for Q6PIL8 (Homo sapiens)
Go to UniProtKB:  Q6PIL8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8f9 Fab
D
242Homo sapiensN/A
Find proteins for Q0ZCI9 (Homo sapiens)
Go to UniProtKB:  Q0ZCI9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.380α = 90.00
b = 76.050β = 90.00
c = 111.540γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata scaling
CNSphasing
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance