4FRW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.2366
  • Primary Citation of Related Structures:  

  • 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 b ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poliovirus receptor-related protein 4
A, B, C, D, E, F
218Homo sapiensMutation(s): 0 
Gene Names: NECTIN4 (LNIR, PRR4, PVRL4)
Find proteins for Q96NY8 (Homo sapiens)
Go to Gene View: NECTIN4
Go to UniProtKB:  Q96NY8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 85.971α = 90.00
b = 142.809β = 90.00
c = 341.802γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-05
    Type: Database references
  • Version 1.2: 2012-09-26
    Type: Database references