9CF6 | pdb_00009cf6

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-CL02.1

• PDB DOI: https://doi.org/10.2210/pdb9CF6/pdb

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


• Deposited: 2024-06-27 Released: 2025-06-25 
• Deposition Author(s): Sarkar, A., Stanfield, R.L., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.306 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.273 (DCC) 

Starting Models: experimental

Literature

Diverse competitor B cell responses to a germline-targeting priming immunogen in human Ig loci transgenic mice

Schiffner, T., Palser, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.57 kDa 
• Atom Count: 4,458 
• Modeled Residue Count: 591 
• Deposited Residue Count: 620 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab eOD-CL02.1 heavy chain	A [auth H]	221	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab eOD-CL02.1 lambda light chain	B [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline-targeting HIV-1 gp120 engineered outer domain eODgt8	C [auth G]	183	Human immunodeficiency virus 1	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.306 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.273 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.039	α = 90
b = 72.601	β = 107.52
c = 93.817	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Sarkar, A., Stanfield, R.L., 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	UM1 AI144462

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release