4ZTO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • 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 i ...

    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
RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
L, M
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
H, I
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Epitope of rabbit monoclonal antibody R53
P, Q
15Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.283α = 90.00
b = 84.831β = 90.00
c = 167.237γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 DiseasesUnited StatesAI082274
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI082676
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI065250
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100151

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description