3EYQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.250 
  • R-Value Observed: 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, 3EYQ, 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 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M2J5 FabA [auth C]216Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PIL8 (Homo sapiens)
Explore Q6PIL8 
Go to UniProtKB:  Q6PIL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PIL8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
8f9 FabB [auth D]242Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q0ZCI9 (Homo sapiens)
Explore Q0ZCI9 
Go to UniProtKB:  Q0ZCI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZCI9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.38α = 90
b = 76.05β = 90
c = 111.54γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
CNSrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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