5W4L

Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region.

Tolbert, W.D.Gohain, N.Alsahafi, N.Van, V.Orlandi, C.Ding, S.Martin, L.Finzi, A.Lewis, G.K.Ray, K.Pazgier, M.

(2017) Structure 25: 1719-1731.e4

  • DOI: 10.1016/j.str.2017.09.009

  • PubMed Abstract: 
  • Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is ...

    Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is recognized by the C11 antibody. Here, we present the crystal structure, at 2.9 Å resolution, of the C11-like antibody N12-i3, in a quaternary complex with the HIV-1 gp120, a CD4-mimicking peptide M48U1, and an A32-like antibody, N5-i5. Antibody N12-i3 recognizes an epitope centered on the N-terminal "eighth strand" of a critical β sandwich, which our analysis indicates to be emblematic of a late-entry state, after the gp120 detachment. In prior entry states, this sandwich comprises only seven strands, with the eighth strand instead pairing with a portion of the gp120 C terminus. The conformational gymnastics of HIV-1 gp120 thus includes altered β-strand pairing, possibly to reduce immunogenicity, although nevertheless still recognized by the human immune system.


    Organizational Affiliation

    Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada; CEA, Joliot, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France.,Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.,CEA, Joliot, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France.,Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada.,Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.,Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA. Electronic address: mpazgier@ihv.umaryland.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
clade A/E 93TH057 HIV-1 gp120 core
G, A
385Human immunodeficiency virus 1Mutation(s): 1 
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Go to UniProtKB:  A0A0M3KKW9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CD4 mimetic peptide M48U1
N, M
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody N5-i5 Fab heavy chain
H, F
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Antibody N5-i5 light chain
L, I
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Antibody N12-i3 Fab heavy chain
D, B
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Antibody N12-i3 light chain
E, C
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, N
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001094
Query on PRD_001094
M,NCD4-MIMETIC MINIPROTEIN M48U1Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 311.018α = 90.00
b = 53.291β = 128.89
c = 223.577γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI116274

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-18
    Type: Data collection
  • Version 1.3: 2018-05-30
    Type: Data collection, Structure summary
  • Version 1.4: 2019-12-11
    Type: Author supporting evidence