9CF7 | pdb_00009cf7

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-PL01.1

PDB DOI: https://doi.org/10.2210/pdb9CF7/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.55 Å
R-Value Free:
0.299 (Depositor), 0.310 (DCC)
R-Value Work:
0.265 (Depositor), 0.269 (DCC)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 66.88 kDa
Atom Count: 4,505
Modeled Residue Count: 593
Deposited Residue Count: 619
Unique protein chains: 3

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab eOD-PL01.1 heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab eOD-PL01.1 kappa light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth C] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C]	D [auth C], E [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.55 Å
R-Value Free: 0.299 (Depositor), 0.310 (DCC)
R-Value Work: 0.265 (Depositor), 0.269 (DCC)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.767	α = 90
b = 166.767	β = 90
c = 100.693	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Stanfield, R.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.