8ZPM | pdb_00008zpm

Cryo-EM strucutre of CXCR4 complexed with antagonist AMD070

• PDB DOI: https://doi.org/10.2210/pdb8ZPM/pdb
• EM Map EMD-60349: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-05-30 Released: 2025-02-26 
• Deposition Author(s): Jiao, H.Z., Hu, H.L.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Mechanisms Underlying the Modulation of CXCR4 by Diverse Antagonists.

Sang, X.H., Jiao, H.Z., Huang, Z.W., Hu, H.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 75.24 kDa 
• Atom Count: 3,222 
• Modelled Residue Count: 398 
• Deposited Residue Count: 655 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,C-X-C chemokine receptor type 4	A [auth R]	486	Escherichia coli, Homo sapiens	Mutation(s): 0  Gene Names: cybC, 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
Nb6 nanobody	B [auth N]	169	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth R], E [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
A1D8L (Subject of Investigation/LOI)	C [auth R]	(S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine C21 H27 N5 WVLHHLRVNDMIAR-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Jiao, H.Z., Hu, H.L.

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Funding Organization	Location	Grant Number
Other government	China	32100963

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release