2N54 | pdb_00002n54

Solution structure of a disulfide stabilized XCL1 dimer


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 2N54

This is version 1.4 of the entry. See complete history

Literature

Engineering Metamorphic Chemokine Lymphotactin/XCL1 into the GAG-Binding, HIV-Inhibitory Dimer Conformation.

Fox, J.C.Tyler, R.C.Guzzo, C.Tuinstra, R.L.Peterson, F.C.Lusso, P.Volkman, B.F.

(2015) ACS Chem Biol 10: 2580-2588

  • DOI: https://doi.org/10.1021/acschembio.5b00542
  • Primary Citation Related Structures: 
    2N54

  • PubMed Abstract: 

    Unlike other chemokines, XCL1 undergoes a distinct metamorphic interconversion between a canonical monomeric chemokine fold and a unique β-sandwich dimer. The monomeric conformation binds and activates the receptor XCR1, whereas the dimer binds extracellular matrix glycosaminoglycans and has been associated with anti-human immunodeficiency virus (HIV) activity. Functional studies of WT-XCL1 are complex, as both conformations are populated in solution. To overcome this limitation, we engineered a stabilized dimeric variant of XCL1 designated CC5. This variant features a new disulfide bond (A36C-A49C) that prevents structural interconversion by locking the chemokine into the β-sandwich dimeric conformation, as demonstrated by NMR structural analysis and hydrogen/deuterium exchange experiments. Functional studies analyzing glycosaminoglycan binding demonstrate that CC5 binds with high affinity to heparin. In addition, CC5 exhibits potent inhibition of HIV-1 activity in primary peripheral blood mononuclear cells (PBMCs), demonstrating the importance of the dimer in blocking viral infection. Conformational variants like CC5 are valuable tools for elucidating the biological relevance of the XCL1 native-state interconversion and will assist in future antiviral and functional studies.


  • Organizational Affiliation
    • Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States.

Macromolecule Content 

  • Total Structure Weight: 20.7 kDa 
  • Atom Count: 1,040 
  • Modeled Residue Count: 132 
  • Deposited Residue Count: 186 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lymphotactin
A, B
93Homo sapiensMutation(s): 2 
Gene Names: XCL1LTNSCYC1
UniProt & NIH Common Fund Data Resources
Find proteins for P47992 (Homo sapiens)
Explore P47992 
Go to UniProtKB:  P47992
PHAROS:  P47992
GTEx:  ENSG00000143184 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47992
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Structure summary