6O42

Crystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in complex with MPER peptide epitope.

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2019-02-27 Released: 2019-12-04 
  • Deposition Author(s): Irimia, A., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An MPER antibody neutralizes HIV-1 using germline features shared among donors.

Zhang, L.Irimia, A.He, L.Landais, E.Rantalainen, K.Leaman, D.P.Vollbrecht, T.Stano, A.Sands, D.I.Kim, A.S.Poignard, P.Burton, D.R.Murrell, B.Ward, A.B.Zhu, J.Wilson, I.A.Zwick, M.B.

(2019) Nat Commun 10: 5389-5389

  • DOI: 10.1038/s41467-019-12973-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, ...

    The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC 50 ). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.


    Organizational Affiliation

    Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA.,Departments of Medicine, Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA.,CTK Biotech, Inc., 3855 Stowe Drive, Poway, California, 92064, USA.,Department of Medicine, University of California, San Diego, California, 92093, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA. wilson@scripps.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA. jiang@scripps.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044, Grenoble, France.,Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachussetts, 02114, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA. wilson@scripps.edu.,Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA. wilson@scripps.edu.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA. zwick@scripps.edu.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA. jiang@scripps.edu.,International AIDS Vaccine Initiative, New York, New York, 10004, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037, USA. wilson@scripps.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PGZL1_gVmDmJ light chain
L, A
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PGZL1_gVmDmJ heavy chain
H, B
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MPER peptide, region 671-683 of HIV-1 gp41
G, I
16N/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
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 208.360α = 90.00
b = 37.920β = 93.68
c = 133.520γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

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 StatesUM1 AI100663

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Type: Database references