2LWL | pdb_00002lwl

Structural Basis for the Interaction of Human β-Defensin 6 and Its Putative Chemokine Receptor CCR2 and Breast Cancer Microvesicles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Basis for the Interaction of Human beta-Defensin 6 and Its Putative Chemokine Receptor CCR2 and Breast Cancer Microvesicles.

De Paula, V.S.Gomes, N.S.Lima, L.G.Miyamoto, C.A.Monteiro, R.Q.Almeida, F.C.Valente, A.P.

(2013) J Mol Biology 425: 4479-4495

  • DOI: https://doi.org/10.1016/j.jmb.2013.08.001
  • Primary Citation Related Structures: 
    2LWL

  • PubMed Abstract: 

    Human β-defensins (hBDs) are believed to function as alarm molecules that stimulate the adaptive immune system when a threat is present. In addition to its antimicrobial activity, defensins present other activities such as chemoattraction of a range of different cell types to the sites of inflammation. We have solved the structure of the hBD6 by NMR spectroscopy that contains a conserved β-defensin domain followed by an extended C-terminus. We use NMR to monitor the interaction of hBD6 with microvesicles shed by breast cancer cell lines and with peptides derived from the extracellular domain of CC chemokine receptor 2 (Nt-CCR2) possessing or not possessing sulfation on Tyr26 and Tyr28. The NMR-derived model of the hBD6/CCR2 complex reveals a contiguous binding surface on hBD6, which comprises amino acid residues of the α-helix and β2-β3 loop. The microvesicle binding surface partially overlaps with the chemokine receptor interface. NMR spin relaxation suggests that free hBD6 and the hBD6/CCR2 complex exhibit microsecond-to-millisecond conformational dynamics encompassing the CCR2 binding site, which might facilitate selection of the molecular configuration optimal for binding. These data offer new insights into the structure-function relation of the hBD6-CCR2 interaction, which is a promising target for the design of novel anticancer agents.


  • Organizational Affiliation
    • Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.

Macromolecule Content 

  • Total Structure Weight: 5.44 kDa 
  • Atom Count: 346 
  • Modeled Residue Count: 45 
  • Deposited Residue Count: 49 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-defensin 10649Homo sapiensMutation(s): 1 
Gene Names: DEFB106ABD6DEFB106DEFB6DEFB106B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N104 (Homo sapiens)
Explore Q8N104 
Go to UniProtKB:  Q8N104
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N104
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2013-11-13
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary