2QHR

Crystal structure of the 13F6-1-2 Fab fragment bound to its Ebola virus glycoprotein peptide epitope.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Complex of a protective antibody with its Ebola virus GP peptide epitope: unusual features of a V lambda x light chain.

Lee, J.E.Kuehne, A.Abelson, D.M.Fusco, M.L.Hart, M.K.Saphire, E.O.

(2008) J Mol Biol 375: 202-216

  • DOI: 10.1016/j.jmb.2007.10.017
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 13F6-1-2 is a murine monoclonal antibody that recognizes the heavily glycosylated mucin-like domain of the Ebola virus virion-attached glycoprotein (GP) and protects animals against lethal viral challenge. Here we present the crystal structure, at 2. ...

    13F6-1-2 is a murine monoclonal antibody that recognizes the heavily glycosylated mucin-like domain of the Ebola virus virion-attached glycoprotein (GP) and protects animals against lethal viral challenge. Here we present the crystal structure, at 2.0 A, of 13F6-1-2 in complex with its Ebola virus GP peptide epitope. The GP peptide binds in an extended conformation, anchored primarily by interactions with the heavy chain. Two GP residues, Gln P406 and Arg P409, make extensive side-chain hydrogen bond and electrostatic interactions with the antibody and are likely critical for recognition and affinity. The 13F6-1-2 antibody utilizes a rare V lambda(x) light chain. The three light-chain complementarity-determining regions do not adopt canonical conformations and represent new classes of structures distinct from V kappa and other V lambda light chains. In addition, although V lambda(x) had been thought to confer specificity, all light-chain contacts are mediated through germ-line-encoded residues. This structure of an antibody that protects against the Ebola virus now provides a framework for humanization and development of a postexposure immunotherapeutic.


    Organizational Affiliation

    Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
13F6-1-2 Fab fragment heavy chainH222Mus musculusMutation(s): 0 
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
13F6-1-2 Fab fragment V lambda x light chainL218Mus musculusMutation(s): 0 
Gene Names: Iglc2
Find proteins for P01844 (Mus musculus)
Explore P01844 
Go to UniProtKB:  P01844
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein peptideP11N/AMutation(s): 0 
Find proteins for P87671 (Zaire ebolavirus (strain Eckron-76))
Explore P87671 
Go to UniProtKB:  P87671
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.24α = 90
b = 70.3β = 90
c = 142.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description