3OE0 | pdb_00003oe0

Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15

• PDB DOI: https://doi.org/10.2210/pdb3OE0/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE/ANTIBIOTIC
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2010-08-12 Released: 2010-10-27 
• Deposition Author(s): Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.

Wu, B., Chien, E.Y., Mol, C.D., Fenalti, G., Liu, W., Katritch, V., Abagyan, R., Brooun, A., Wells, P., Bi, F.C., Hamel, D.J., Kuhn, P., Handel, T.M., Cherezov, V., Stevens, R.C.

(2010) Science 330: 1066-1071

• PubMed: 20929726 
• DOI: https://doi.org/10.1126/science.1194396
• Primary Citation Related Structures: 
  3ODU, 3OE0, 3OE6, 3OE8, 3OE9


• PubMed Abstract: 
  

  Chemokine receptors are critical regulators of cell migration in the context of immune surveillance, inflammation, and development. The G protein-coupled chemokine receptor CXCR4 is specifically implicated in cancer metastasis and HIV-1 infection. Here we report five independent crystal structures of CXCR4 bound to an antagonist small molecule IT1t and a cyclic peptide CVX15 at 2.5 to 3.2 angstrom resolution. All structures reveal a consistent homodimer with an interface including helices V and VI that may be involved in regulating signaling. The location and shape of the ligand-binding sites differ from other G protein-coupled receptors and are closer to the extracellular surface. These structures provide new clues about the interactions between CXCR4 and its natural ligand CXCL12, and with the HIV-1 glycoprotein gp120.

---

Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.83 kDa 
• Atom Count: 3,640 
• Modeled Residue Count: 449 
• Deposited Residue Count: 515 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4, Lysozyme Chimera	A	499	Homo sapiens, Tequatrovirus T4	Mutation(s): 4  Gene Names: CXCR4, CXCR4_HUMAN, E EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P61073 (Homo sapiens) Explore P61073  Go to UniProtKB:  P61073
PHAROS:  P61073 GTEx:  ENSG00000121966
UniProt Groups	P00720P61073

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphemusin analog, CXC chemokine receptor antagonist	B [auth I]	16	N/A	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALN	B [auth I]	L-PEPTIDE LINKING	C13 H13 N O2		ALA
CIR	B [auth I]	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG
DPR	B [auth I]	D-PEPTIDE LINKING	C5 H9 N O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001107	B [auth I]	Polyphemusin analog, CXC chemokine receptor antagonist	Oligopeptide / Antagonist

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.08	α = 90
b = 144.86	β = 104.54
c = 73.99	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-02
  Changes: Structure summary
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.5: 2021-10-06
  Changes: Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations