4ZTP

Fab structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region

  • Classification: IMMUNE SYSTEM
  • Organism(s): Oryctolagus cuniculus
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2015-05-14 Released: 2015-08-19 
  • Deposition Author(s): Pan, R., Kong, X.-P.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding.

Pan, R.Chen, Y.Vaine, M.Hu, G.Wang, S.Lu, S.Kong, X.P.

(2015) Emerg Microbes Infect 4: e44-e44

  • DOI: 10.1038/emi.2015.44
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The fourth conserved region (C4) in the HIV-1 envelope glycoprotein (Env) gp120 is a structural element that is important for its function, as it binds to both the receptor CD4 and the co-receptor CCR5/CXCR4. It has long been known that this region is highly immunogenic and that it harbors B-cell as well as T-cell epitopes ...

    The fourth conserved region (C4) in the HIV-1 envelope glycoprotein (Env) gp120 is a structural element that is important for its function, as it binds to both the receptor CD4 and the co-receptor CCR5/CXCR4. It has long been known that this region is highly immunogenic and that it harbors B-cell as well as T-cell epitopes. It is the target of a number of antibodies in animal studies, which are called CD4-blockers. However, the mechanism by which the virus shields itself from such antibody responses is not known. Here, we determined the crystal structure of R53 in complex with its epitope peptide using a novel anti-C4 rabbit monoclonal antibody R53. Our data show that although the epitope of R53 covers a highly conserved sequence (433)AMYAPPI(439), it is not available in the gp120 trimer and in the CD4-bound conformation. Our results suggest a masking mechanism to explain how HIV-1 protects this critical region from the human immune system.


    Organizational Affiliation

    Departments of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, NY 10016, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab fragment of rabbit monoclonal antibody R53L216Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab fragment of rabbit monoclonal antibody R53H223Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.433α = 90
b = 78.553β = 92.25
c = 68.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-05-14 
  • Released Date: 2015-08-19 
  • Deposition Author(s): Pan, R., Kong, X.-P.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI082274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI082676
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI065250
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI100151

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence