4H5S | pdb_00004h5s

Complex structure of Necl-2 and CRTAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4H5S

This is version 1.3 of the entry. See complete history

Literature

Competition of cell adhesion and immune recognition: insights into the interaction between CRTAM and nectin-like 2.

Zhang, S.Lu, G.Qi, J.Li, Y.Zhang, Z.Zhang, B.Fan, Z.Yan, J.Gao, G.F.

(2013) Structure 21: 1430-1439

  • DOI: https://doi.org/10.1016/j.str.2013.06.006
  • Primary Citation Related Structures: 
    4H5S

  • PubMed Abstract: 

    Nectin and nectin-like proteins are cell adhesion molecules that mediate the formation of cell adherens junctions by forming homo- or heterodimers. Some members of this protein family can also be used by immune receptors to mediate immune recognition. For instance, nectin-like 2 (Necl-2) is used as a ligand for the immune system by interaction with the immune receptor CRTAM (class-I MHC-restricted T cell associated molecule), which is mainly expressed on the surface of cytotoxic lymphocyte cells. However, the Necl-2/CRTAM binding mode and its relationship to cell adhesion are not known. Here, we report a Necl-2/CRTAM complex structure, demonstrating that Necl-2 binding to CRTAM competes with the dimerization of CRTAM and possibly Necl-2. Necl-2 occupies the CRTAM homodimer interface, making homodimerization impossible. Mutational and functional analyses identified key amino acids (double "lock-and-key") responsible for the binding. Our work illustrates how the cell adhesion molecule Necl-2 competitively binds the immune receptor CRTAM.


  • Organizational Affiliation
    • School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

Macromolecule Content 

  • Total Structure Weight: 22.87 kDa 
  • Atom Count: 1,939 
  • Modeled Residue Count: 196 
  • Deposited Residue Count: 202 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytotoxic and regulatory T-cell molecule101Homo sapiensMutation(s): 0 
Gene Names: CRTAM
UniProt & NIH Common Fund Data Resources
Find proteins for O95727 (Homo sapiens)
Explore O95727 
Go to UniProtKB:  O95727
PHAROS:  O95727
GTEx:  ENSG00000109943 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95727
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell adhesion molecule 1101Homo sapiensMutation(s): 0 
Gene Names: CADM1IGSF4IGSF4ANECL2SYNCAMTSLC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY67 (Homo sapiens)
Explore Q9BY67 
Go to UniProtKB:  Q9BY67
PHAROS:  Q9BY67
GTEx:  ENSG00000182985 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY67
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.042α = 90
b = 91.042β = 90
c = 56.684γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
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: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Derived calculations
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary