4YC2

Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in complex with the antibody A32.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.

Tolbert, W.D.Gohain, N.Veillette, M.Chapleau, J.P.Orlandi, C.Visciano, M.L.Ebadi, M.DeVico, A.L.Fouts, T.R.Finzi, A.Lewis, G.K.Pazgier, M.

(2016) Structure 24: 697-709

  • DOI: 10.1016/j.str.2016.03.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Evidence supports a role of antibody-dependent cellular cytotoxicity (ADCC) toward transitional epitopes in the first and second constant (C1-C2) regions of gp120 (A32-like epitopes) in preventing HIV-1 infection and in vaccine-induced protection. He ...

    Evidence supports a role of antibody-dependent cellular cytotoxicity (ADCC) toward transitional epitopes in the first and second constant (C1-C2) regions of gp120 (A32-like epitopes) in preventing HIV-1 infection and in vaccine-induced protection. Here, we describe the first successful attempt at isolating the inner domain (ID) of gp120 as an independent molecule that encapsulates the A32-like region within a minimal structural unit of the HIV-1 Env. Through structure-based design, we developed ID2, which consists of the ID expressed independently of the outer domain and stabilized in the CD4-bound conformation by an inter-layer disulfide bond. ID2 expresses C1-C2 epitopes in the context of CD4-triggered full-length gp120 but without any known neutralizing epitope present. Thus, ID2 represents a novel probe for the analysis and/or selective induction of antibody responses to the A32 epitope region. We also present the crystal structure of ID2 complexed with mAb A32, which defines its epitope.


    Organizational Affiliation

    Centre de Recherche du CHUM, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H2X 0A9, Canada.,Profectus BioSciences, Inc., Baltimore, MD 21224, USA.,Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA. Electronic address: mpazgier@ihv.umaryland.edu.,Centre de Recherche du CHUM, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada.,Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli
G, A
156Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Go to UniProtKB:  A0A0M3KKW9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
The antibody A32 Fab heavy chain.
H, B
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
The antibody A32 Fab light chain.
L, C
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.801α = 90.00
b = 211.800β = 90.00
c = 72.898γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
REFMACrefinement
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1033109

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Data collection
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence