6O41

Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41467-019-12973-1
  • Primary Citation of Related Structures:  
    6O3D, 6O3G, 6O3J, 6O3K, 6O3L, 6O3U, 6O41, 6O42

  • 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, 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

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
germline PGZL1_gVmDmJ light chainA [auth L],
C [auth A],
E [auth C]
215Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
germline PGZL1_gVmDmJ heavy chainB [auth H],
D [auth B],
F [auth D]
227Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G (DOMAIN III)G [auth M],
H [auth N],
I [auth O]
66Streptococcus sp. 'group GMutation(s): 0 
Gene Names: spg
UniProt
Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
Entity Groups  
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UniProt GroupP19909
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth L]
K [auth L]
L
M [auth L]
N [auth L]
J [auth L],
K [auth L],
L,
M [auth L],
N [auth L],
O [auth H],
P [auth H],
Q [auth A],
R [auth B],
S [auth C],
T [auth C],
U [auth D],
V [auth O]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.84α = 90
b = 107.49β = 94.61
c = 131.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary