9ME1 | pdb_00009me1

hCXCR4-CXCL12 complex with 1:1 stoichiometry

• PDB DOI: https://doi.org/10.2210/pdb9ME1/pdb
• EM Map EMD-48182: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-05 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: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryo-EM structure of CXCR4-CXCL12 complex with 1:2 stoichiometry

Zhang, Z., Patel, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 403.46 kDa 
• Atom Count: 21,155 
• Modeled Residue Count: 2,768 
• Deposited Residue Count: 3,520 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4	A [auth B], B [auth A], E [auth C], F [auth D], G [auth I], H [auth E], I [auth K], J [auth L]	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
Stromal cell-derived factor 1	C [auth N], D [auth O], K [auth P], L [auth M], M [auth J], N [auth F], O [auth G], P [auth H]	80	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, SDF1, SDF1A, SDF1B
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
PHAROS:  P48061 GTEx:  ENSG00000107562

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 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)		P30 CA008748

Revision History  

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