6ULM | pdb_00006ulm

Crystal structure of human cadherin 17 EC1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.257 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6ULM

This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism.

Gray, M.E.Sotomayor, M.

(2021) Acta Crystallogr F Struct Biol Commun 77: 85-94

  • DOI: https://doi.org/10.1107/S2053230X21002247
  • Primary Citation Related Structures: 
    6ULM

  • PubMed Abstract: 

    The cadherin superfamily of calcium-dependent cell-adhesion proteins has over 100 members in the human genome. All members of the superfamily feature at least a pair of extracellular cadherin (EC) repeats with calcium-binding sites in the EC linker region. The EC repeats across family members form distinct complexes that mediate cellular adhesion. For instance, classical cadherins (five EC repeats) strand-swap their N-termini and exchange tryptophan residues in EC1, while the clustered protocadherins (six EC repeats) use an extended antiparallel `forearm handshake' involving repeats EC1-EC4. The 7D-cadherins, cadherin-16 (CDH16) and cadherin-17 (CDH17), are the most similar to classical cadherins and have seven EC repeats, two of which are likely to have arisen from gene duplication of EC1-2 from a classical ancestor. However, CDH16 and CDH17 lack the EC1 tryptophan residue used by classical cadherins to mediate adhesion. The structure of human CDH17 EC1-2 presented here reveals features that are not seen in classical cadherins and that are incompatible with the EC1 strand-swap mechanism for adhesion. Analyses of crystal contacts, predicted glycosylation and disease-related mutations are presented along with sequence alignments suggesting that the novel features in the CDH17 EC1-2 structure are well conserved. These results hint at distinct adhesive properties for 7D-cadherins.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.

Macromolecule Content 

  • Total Structure Weight: 51.62 kDa 
  • Atom Count: 3,401 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cadherin-17A [auth B],
B [auth A]
228Homo sapiensMutation(s): 1 
Gene Names: CDH17
UniProt & NIH Common Fund Data Resources
Find proteins for Q12864 (Homo sapiens)
Explore Q12864 
Go to UniProtKB:  Q12864
PHAROS:  Q12864
GTEx:  ENSG00000079112 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12864
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.257 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.394α = 90
b = 81.609β = 90
c = 106.813γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description