4FMF

Crystal structure of human nectin-1 full ectodomain (D1-D3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.2 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: https://doi.org/10.1038/nsmb.2366
  • Primary Citation of Related Structures:  
    4FMF, 4FMK, 4FN0, 4FOM, 4FQP, 4FRW, 4FS0

  • 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 1
A, B, C, D
313Homo sapiensMutation(s): 0 
Gene Names: PVRL1HVECPRR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15223 (Homo sapiens)
Explore Q15223 
Go to UniProtKB:  Q15223
PHAROS:  Q15223
GTEx:  ENSG00000110400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15223
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q15223-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.288α = 90
b = 106.288β = 90
c = 334.622γ = 120
Software Package:
Software NamePurpose
HKL-2000data 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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary