9ZG9 | pdb_00009zg9

Crystal structure of DH511.12P Fab in complex with HIV-1 gp41 MPER peptide and phosphatidic acid (06:0 PA); single-lipid form

• PDB DOI: https://doi.org/10.2210/pdb9ZG9/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: 2.21 Å
• R-Value Free: 
  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.73 kDa 
• Atom Count: 7,598 
• Modeled Residue Count: 928 
• Deposited Residue Count: 942 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DH511.12P Fab heavy chain	A, D	236	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DH511.12P Fab light chain	B, E	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	C, F	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
44E (Subject of Investigation/LOI)	H [auth B], I [auth B], J [auth E]	(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate C15 H29 O8 P SFZZRGHNPILUOD-CYBMUJFWSA-N
PEG (Subject of Investigation/LOI)	G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.095	α = 90
b = 63.382	β = 97.278
c = 121.398	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