4FRW

Crystal structure of human nectin-4 extracellular fragment D1-D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Nectin ectodomain structures reveal a canonical adhesive interface.

Harrison, O.J.Vendome, J.Brasch, J.Jin, X.Hong, S.Katsamba, P.S.Ahlsen, G.Troyanovsky, R.B.Troyanovsky, S.M.Honig, B.Shapiro, L.

(2012) Nat Struct Mol Biol 19: 906-915

  • DOI: https://doi.org/10.1038/nsmb.2366
  • Primary Citation of Related Structures:  
    4FRW

  • PubMed Abstract: 

    Nectins are immunoglobulin superfamily glycoproteins that mediate intercellular adhesion in many vertebrate tissues. Homophilic and heterophilic interactions between nectin family members help mediate tissue patterning. We determined the homophilic binding affinities and heterophilic specificities of all four nectins and the related protein nectin-like 5 (Necl-5) from human and mouse, revealing a range of homophilic interaction strengths and a defined heterophilic specificity pattern. To understand the molecular basis of their adhesion and specificity, we determined the crystal structures of natively glycosylated full ectodomains or adhesive fragments of all four nectins and Necl-5. All of the crystal structures revealed dimeric nectins bound through a stereotyped interface that was previously proposed to represent a cis dimer. However, conservation of this interface and the results of targeted cross-linking experiments showed that this dimer probably represents the adhesive trans interaction. The structure of the dimer provides a simple molecular explanation for the adhesive binding specificity of nectins.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 4
A, B, C, D, E
A, B, C, D, E, F
218Homo sapiensMutation(s): 0 
Gene Names: PVRL4LNIRPRR4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY8 (Homo sapiens)
Explore Q96NY8 
Go to UniProtKB:  Q96NY8
PHAROS:  Q96NY8
GTEx:  ENSG00000143217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NY8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.971α = 90
b = 142.809β = 90
c = 341.802γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Database references
  • Version 1.2: 2012-09-26
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description