2N0X

Three dimensional structure of EPI-X4, a human albumin-derived peptide that regulates innate immunity through the CXCR4/CXCL12 chemotactic axis and antagonizes HIV-1 entry

• PDB DOI:  https://doi.org/10.2210/pdb2N0X/pdb
• BMRB: 25539

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2015-03-18 Released: 2015-04-29 
• Deposition Author(s): Perez-Castells, J., Canales, A., Jimenez-Barbero, J., Gimenez-Gallego, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Discovery and characterization of an endogenous CXCR4 antagonist.

Zirafi, O., Kim, K.A., Standker, L., Mohr, K.B., Sauter, D., Heigele, A., Kluge, S.F., Wiercinska, E., Chudziak, D., Richter, R., Moepps, B., Gierschik, P., Vas, V., Geiger, H., Lamla, M., Weil, T., Burster, T., Zgraja, A., Daubeuf, F., Frossard, N., Hachet-Haas, M., Heunisch, F., Reichetzeder, C., Galzi, J.L., Perez-Castells, J., Canales-Mayordomo, A., Jimenez-Barbero, J., Gimenez-Gallego, G., Schneider, M., Shorter, J., Telenti, A., Hocher, B., Forssmann, W.G., Bonig, H., Kirchhoff, F., Munch, J.

(2015) Cell Rep 11: 737-747

• PubMed: 25921529 
• DOI: https://doi.org/10.1016/j.celrep.2015.03.061
• Primary Citation of Related Structures:  
  2N0X


• PubMed Abstract: 
  

CXCL12-CXCR4 signaling controls multiple physiological processes and its dysregulation is associated with cancers and inflammatory diseases. To discover as-yet-unknown endogenous ligands of CXCR4, we screened a blood-derived peptide library for inhibitors of CXCR4-tropic HIV-1 strains. This approach identified a 16 amino acid fragment of serum albumin as an effective and highly specific CXCR4 antagonist. The endogenous peptide, termed EPI-X4, is evolutionarily conserved and generated from the highly abundant albumin precursor by pH-regulated proteases. EPI-X4 forms an unusual lasso-like structure and antagonizes CXCL12-induced tumor cell migration, mobilizes stem cells, and suppresses inflammatory responses in mice. Furthermore, the peptide is abundant in the urine of patients with inflammatory kidney diseases and may serve as a biomarker. Our results identify EPI-X4 as a key regulator of CXCR4 signaling and introduce proteolysis of an abundant precursor protein as an alternative concept for chemokine receptor regulation.

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Organizational Affiliation: 

Institute of Molecular Virology, University of Ulm, 89081 Ulm, Germany; Ulm Peptide Pharmaceuticals, University of Ulm, 89081 Ulm, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1.83 kDa 
• Atom Count: 128 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A	16	Homo sapiens	Mutation(s): 0  Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768  Go to UniProtKB:  P02768
PHAROS:  P02768

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Perez-Castells, J., Canales, A., Jimenez-Barbero, J., Gimenez-Gallego, G.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2015-05-20
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Data collection, Database references, Other