4ODX

4E10 germline encoded precursor no.7 in complex with epitope scaffold T117


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10.

Finton, K.A.Friend, D.Jaffe, J.Gewe, M.Holmes, M.A.Larman, H.B.Stuart, A.Larimore, K.Greenberg, P.D.Elledge, S.J.Stamatatos, L.Strong, R.K.

(2014) Plos Pathog. 10: e1004403-e1004403

  • DOI: 10.1371/journal.ppat.1004403
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The process of antibody ontogeny typically improves affinity, on-rate, and thermostability, narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding from the broader ensemble accessible to the precursor. However ...

    The process of antibody ontogeny typically improves affinity, on-rate, and thermostability, narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding from the broader ensemble accessible to the precursor. However, many broadly-neutralizing anti-HIV antibodies incorporate unusual structural elements and recognition specificities or properties that often lead to autoreactivity. The ontogeny of 4E10, an autoreactive antibody with unexpected combining site flexibility, was delineated through structural and biophysical comparisons of the mature antibody with multiple potential precursors. 4E10 gained affinity primarily by off-rate enhancement through a small number of mutations to a highly conserved recognition surface. Controverting the conventional paradigm, the combining site gained flexibility and autoreactivity during ontogeny, while losing thermostability, though polyspecificity was unaffected. Details of the recognition mechanism, including inferred global effects due to 4E10 binding, suggest that neutralization by 4E10 may involve mechanisms beyond simply binding, also requiring the ability of the antibody to induce conformational changes distant from its binding site. 4E10 is, therefore, unlikely to be re-elicited by conventional vaccination strategies.


    Organizational Affiliation

    Department of Immunology, University of Washington, Seattle, Washington, United States of America.,Department of Immunology, University of Washington, Seattle, Washington, United States of America; Department of Medicine, University of Washington, Seattle, Washington, United States of America; Program in Immunology, Cancer Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.,Seattle Biomedical Research Institute, Seattle, Washington, United States of America; Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Genetics, Harvard University Medical School, and Division of Genetics, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.,Seattle Biomedical Research Institute, Seattle, Washington, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4E10 epitope scaffold T117
X, Y
161N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GEP7 Fv heavy chain
A, H
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GEP7 Fv light chain
B, L
113Homo sapiensMutation(s): 0 
Gene Names: IGKV3-20
Find proteins for P01619 (Homo sapiens)
Go to UniProtKB:  P01619
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.280 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.912α = 90.00
b = 78.004β = 112.29
c = 78.396γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-10 
  • Released Date: 2014-10-08 
  • Deposition Author(s): Finton, K.A.K.

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release