9MEN | pdb_00009men

CryoEM structure of hCXCR4 tetramer bound to HIV-2/gp120/V3 loop

• PDB DOI: https://doi.org/10.2210/pdb9MEN/pdb
• EM Map EMD-48218: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Virus-associated RNAs
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-07 Released: 2025-09-10 
• Deposition Author(s): Zhang, Z., Patel, D.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryoEM structure of hCXCR4 tetramer bound to HIV-2/gp120/V3 loop

Zhang, Z., Patel, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 165.4 kDa 
• Atom Count: 9,281 
• Modeled Residue Count: 1,144 
• Deposited Residue Count: 1,460 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4	A, B, C, D	360	Homo sapiens	Mutation(s): 0  Gene Names: CXCR4
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens) Explore P61073  Go to UniProtKB:  P61073
PHAROS:  P61073 GTEx:  ENSG00000121966

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	E	20	Virus-associated RNAs	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for P05883 (Human immunodeficiency virus type 2 subtype A (isolate NIH-Z)) Explore P05883  Go to UniProtKB:  P05883

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Zhang, Z., Patel, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30 CA008748

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release