6MNQ

Rhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 peptide

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2018-10-02 Released: 2019-07-24 
  • Deposition Author(s): Nicely, N.I.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.804 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations.

Han, Q.Jones, J.A.Nicely, N.I.Reed, R.K.Shen, X.Mansouri, K.Louder, M.Trama, A.M.Alam, S.M.Edwards, R.J.Bonsignori, M.Tomaras, G.D.Korber, B.Montefiori, D.C.Mascola, J.R.Seaman, M.S.Haynes, B.F.Saunders, K.O.

(2019) Nat Commun 10: 2898-2898

  • DOI: 10.1038/s41467-019-10899-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HIV-1 envelope (Env) is the target for neutralizing antibodies and exists on the surface of virions in open or closed conformations. Difficult-to-neutralize viruses (tier 2) express Env in a closed conformation antigenic for broadly neutralizing ...

    The HIV-1 envelope (Env) is the target for neutralizing antibodies and exists on the surface of virions in open or closed conformations. Difficult-to-neutralize viruses (tier 2) express Env in a closed conformation antigenic for broadly neutralizing antibodies (bnAbs) but not for third variable region (V3) antibodies. Here we show that select V3 macaque antibodies elicited by Env vaccination can neutralize 26% of otherwise tier 2 HIV-1 isolates in standardized virus panels. The V3 antibodies only bound to Env in its open conformation. Thus, Envs on tier 2 viruses sample a state where the V3 loop is not in its closed conformation position. Envelope second variable region length, glycosylation sites and V3 amino acids were signatures of neutralization sensitivity. This study determined that open conformations of Env with V3 exposed are present on a subset of otherwise neutralization-resistant virions, therefore neutralization of tier 2 HIV-1 does not always indicate bnAb induction.


    Organizational Affiliation

    Center for Virology and Vaccine Research, Israel Deaconess Medical Center, Boston, MA, 02115, USA.,Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. Kevin.saunders@duke.edu.,Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Immunology, Duke University Medical Center, Durham, NC, 27710, USA.,Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. Barton.haynes@dm.duke.edu.,Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA. Barton.haynes@dm.duke.edu.,Department of Immunology, Duke University Medical Center, Durham, NC, 27710, USA. Barton.haynes@dm.duke.edu.,Department of Immunology, Duke University Medical Center, Durham, NC, 27710, USA. Kevin.saunders@duke.edu.,Department of Microbiology and Molecular Genetics, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Vaccine Research Center, National Instiftute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA.,Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA. Kevin.saunders@duke.edu.,Department of Microbiology and Molecular Genetics, Duke University Medical Center, Durham, NC, 27710, USA. Kevin.saunders@duke.edu.,Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
P
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ab DH727.2 heavy chain Fab fragment
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ab DH727.2 light chain
L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
L, P
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.804 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.511α = 90.00
b = 95.780β = 92.67
c = 58.049γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-02 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Nicely, N.I.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01-AI120801
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesUM1-AI100645

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release