3EYF

Crystal structure of anti-human cytomegalovirus antibody 8f9 plus gB peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3F12, 3EYF, 3EYO, 3EYQ

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
8f9 FabA, C216Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PJF2 (Homo sapiens)
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Go to UniProtKB:  Q6PJF2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AD-2B, D242Homo sapiensMutation(s): 0 
Gene Names: DKFZp686E23209
UniProt
Find proteins for Q68CN4 (Homo sapiens)
Explore Q68CN4 
Go to UniProtKB:  Q68CN4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Synthetic peptideE, F11N/AMutation(s): 1 
UniProt
Find proteins for P13201 (Human cytomegalovirus (strain Towne))
Explore P13201 
Go to UniProtKB:  P13201
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth C], H [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.3α = 90
b = 103.5β = 90
c = 152.5γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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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: Non-polymer description, Version format compliance
  • Version 1.2: 2017-07-05
    Changes: Database references