4P79 | pdb_00004p79

Crystal structure of mouse claudin-15

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of a claudin provides insight into the architecture of tight junctions.

Suzuki, H., Nishizawa, T., Tani, K., Yamazaki, Y., Tamura, A., Ishitani, R., Dohmae, N., Tsukita, S., Nureki, O., Fujiyoshi, Y.

(2014) Science 344: 304-307

  • DOI: https://doi.org/10.1126/science.1248571
  • Primary Citation Related Structures: 
    4P79

  • PubMed Abstract: 

    Tight junctions are cell-cell adhesion structures in epithelial cell sheets that surround organ compartments in multicellular organisms and regulate the permeation of ions through the intercellular space. Claudins are the major constituents of tight junctions and form strands that mediate cell adhesion and function as paracellular barriers. We report the structure of mammalian claudin-15 at a resolution of 2.4 angstroms. The structure reveals a characteristic β-sheet fold comprising two extracellular segments, which is anchored to a transmembrane four-helix bundle by a consensus motif. Our analyses suggest potential paracellular pathways with distinctive charges on the extracellular surface, providing insight into the molecular basis of ion homeostasis across tight junctions.

    • Organizational Affiliation: 
    • Cellular and Structural Physiology Institute, Nagoya University, Chikusa, Nagoya 464-8601, Japan.

Macromolecule Content 

  • Total Structure Weight: 22.16 kDa 
  • Atom Count: 1,391 
  • Modeled Residue Count: 181 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Claudin-15198Mus musculusMutation(s): 4 
Gene Names: Cldn15
Membrane Entity: Yes 
UniProt
Find proteins for Q9Z0S5 (Mus musculus)
Explore Q9Z0S5 
Go to UniProtKB:  Q9Z0S5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z0S5
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.25α = 90
b = 28.403β = 100.84
c = 58.587γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Derived calculations
  • Version 1.2: 2017-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary