4R4F

Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.

Acharya, P.Tolbert, W.D.Gohain, N.Wu, X.Yu, L.Liu, T.Huang, W.Huang, C.C.Kwon, Y.D.Louder, R.K.Luongo, T.S.McLellan, J.S.Pancera, M.Yang, Y.Zhang, B.Flinko, R.Foulke, J.S.Sajadi, M.M.Kamin-Lewis, R.Robinson, J.E.Martin, L.Kwong, P.D.Guan, Y.DeVico, A.L.Lewis, G.K.Pazgier, M.

(2014) J.Virol. 88: 12895-12906

  • DOI: 10.1128/JVI.02194-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RV144 vaccine trial implicated epitopes in the C1 region of gp120 (A32-like epitopes) as targets of potentially protective antibody-dependent cellular cytotoxicity (ADCC) responses. A32-like epitopes are highly immunogenic, as infected or vaccina ...

    The RV144 vaccine trial implicated epitopes in the C1 region of gp120 (A32-like epitopes) as targets of potentially protective antibody-dependent cellular cytotoxicity (ADCC) responses. A32-like epitopes are highly immunogenic, as infected or vaccinated individuals frequently produce antibodies specific for these determinants. Antibody titers, as measured by enzyme-linked immunosorbent assay (ELISA) against these epitopes, however, do not consistently correlate with protection. Here, we report crystal structures of CD4-stabilized gp120 cores complexed with the Fab fragments of two nonneutralizing, A32-like monoclonal antibodies (MAbs), N5-i5 and 2.2c, that compete for antigen binding and have similar antigen-binding affinities yet exhibit a 75-fold difference in ADCC potency. We find that these MAbs recognize overlapping epitopes formed by mobile layers 1 and 2 of the gp120 inner domain, including the C1 and C2 regions, but bind gp120 at different angles via juxtaposed VH and VL contact surfaces. A comparison of structural and immunological data further showed that antibody orientation on bound antigen and the capacity to form multivalent antigen-antibody complexes on target cells were key determinants of ADCC potency, with the latter process having the greater impact. These studies provide atomic-level definition of A32-like epitopes implicated as targets of protective antibodies in RV144. Moreover, these studies establish that epitope structure and mode of antibody binding can dramatically affect the potency of Fc-mediated effector function against HIV-1. These results provide key insights for understanding, refining, and improving the outcome of HIV vaccine trials, in which relevant immune responses are facilitated by A32-like elicited responses.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA Medical Care Clinical Center, VA Maryland Health Care Center, Baltimore, Maryland, USA.,Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA mpazgier@ihv.umaryland.edu.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA.,CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Env gp120
A
376Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)Mutation(s): 0 
Gene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Go to UniProtKB:  P35961
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody 2.2c LIGHT CHAIN
L
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody 2.2c heavy CHAIN
H
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
M48U1 peptide
R
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, L
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, H
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
RCD4-MIMETIC MINIPROTEIN M48U1Peptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OAS
Query on OAS
L
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 158.321α = 90.00
b = 171.230β = 90.00
c = 227.974γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Structure summary
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Experimental preparation