8GBW | pdb_00008gbw

Crystal structure of PC39-23D, an anti-HIV broadly neutralizing antibody

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-02-28 Released: 2023-06-07 
  • Deposition Author(s): Murrell, S., Omorodion, O., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8GBW

This is version 1.3 of the entry. See complete history

Literature

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.

Joyce, C.Murrell, S.Murrell, B.Omorodion, O.Ver, L.S.Carrico, N.Bastidas, R.Nedellec, R.Bick, M.Woehl, J.Zhao, F.Burns, A.Barman, S.Appel, M.Ramos, A.Wickramasinghe, L.Eren, K.Vollbrecht, T.Smith, D.M.Kosakovsky Pond, S.L.McBride, R.Worth, C.Batista, F.Sok, D.Poignard, P.Briney, B.Wilson, I.A.Landais, E.Burton, D.R.

(2023) PLoS Pathog 19: e1011416-e1011416

  • DOI: https://doi.org/10.1371/journal.ppat.1011416
  • Primary Citation Related Structures: 
    8GBV, 8GBW, 8GBX, 8GBY, 8GBZ, 8GC0, 8GC1

  • PubMed Abstract: 

    Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population "arms" that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America.

Macromolecule Content 

  • Total Structure Weight: 51.15 kDa 
  • Atom Count: 4,463 
  • Modeled Residue Count: 458 
  • Deposited Residue Count: 461 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PC39-23D Fab heavy chainA [auth H]243Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PC39-23D Fab light chainB [auth L]218Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth H],
J [auth H],
K [auth H]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth H]
D [auth H]
E [auth H]
F [auth H]
G [auth H]
C [auth H],
D [auth H],
E [auth H],
F [auth H],
G [auth H],
H,
L,
M [auth L],
N [auth L],
O [auth L],
P [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.284α = 90
b = 83.367β = 90
c = 151.767γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462
Bill & Melinda Gates FoundationUnited StatesOPP119635

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection
  • Version 1.3: 2024-10-23
    Changes: Structure summary