9ZGD | pdb_00009zgd

Crystal structure of VRC42.01 Fab in the presence of HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); unliganded form

• PDB DOI: https://doi.org/10.2210/pdb9ZGD/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-12-02 Released: 2026-07-08 
• Deposition Author(s): Cho, S.Y., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structural basis of membrane engagement and polyreactivity control in HIV-1 MPER broadly neutralizing antibodies

Cho, S.Y., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.9 kDa 
• Atom Count: 3,444 
• Modeled Residue Count: 453 
• Deposited Residue Count: 460 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody VRC42.01 Fab heavy chain	A	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody VRC42.01 Fab light chain	B	213	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	C	19	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q73372 (Human immunodeficiency virus type 1 group M subtype B (strain 89.6)) Explore Q73372  Go to UniProtKB:  Q73372

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.443	α = 90
b = 73.524	β = 99.43
c = 44.214	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-08 
Deposition Author(s): Cho, S.Y., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI144462
Bill & Melinda Gates Foundation	United States	INV-007522
Bill & Melinda Gates Foundation	United States	INV-008813

Revision History  

• Version 1.0: 2026-07-08
  Type: Initial release