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- PDB-7kp4: Crystal structure of human claudin-4 in complex with Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 7kp4
TitleCrystal structure of human claudin-4 in complex with Clostridium perfringens enterotoxin C-terminal domain
Components
  • Claudin-4
  • Heat-labile enterotoxin B chain
KeywordsCELL ADHESION/TOXIN / Claudin / Enterotoxin / Tight junction protein / Transmembrane protein / CELL ADHESION-TOXIN complex
Function / homology
Function and homology information


positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity ...positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity / chloride channel complex / lateral plasma membrane / bicellular tight junction / establishment of skin barrier / basal plasma membrane / response to progesterone / female pregnancy / circadian rhythm / transmembrane signaling receptor activity / cell-cell junction / toxin activity / cell adhesion / positive regulation of cell migration / apical plasma membrane / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-4 / Claudin / Claudin, conserved site / Claudin family signature. / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily
Similarity search - Domain/homology
Claudin-4 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsVecchio, A.J. / Stroud, R.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138368 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM024485 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for Clostridium perfringens enterotoxin targeting of claudins at tight junctions in mammalian gut.
Authors: Vecchio, A.J. / Rathnayake, S.S. / Stroud, R.M.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Claudin-4
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)37,7292
Polymers37,7292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-9 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 116.230, 118.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Claudin-4 / Clostridium perfringens enterotoxin receptor / CPE-receptor / Williams-Beuren syndrome chromosomal ...Clostridium perfringens enterotoxin receptor / CPE-receptor / Williams-Beuren syndrome chromosomal region 8 protein


Mass: 22613.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLDN4, CPER, CPETR1, WBSCR8 / Plasmid: pFastBac1 / Cell line (production host): Tni / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14493
#2: Protein Heat-labile enterotoxin B chain


Mass: 15114.945 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 192-319)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Plasmid: pFastBac1 / Cell line (production host): Tni / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01558

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.49 Å3/Da / Density % sol: 81.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM DL-malic acid + MES + Tris base (1:2:2), pH 6.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 3.365→59.03 Å / Num. obs: 26037 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 156.9 Å2 / CC1/2: 1 / CC star: 1 / Rrim(I) all: 0.063 / Net I/σ(I): 8.11
Reflection shellResolution: 3.365→3.449 Å / Redundancy: 2.56 % / Mean I/σ(I) obs: 0.29 / Num. unique obs: 1756 / CC1/2: 0.139 / CC star: 0.139 / Rrim(I) all: 5.94 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDS20180427data reduction
XSCALE20180427data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ov2 poly(ALA) and displaced cCpE from 6ov2

6ov2

6ov2


Resolution: 3.37→44.81 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 1908 7.83 %
Rwork0.294 --
obs0.294 24373 91.8 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.37→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 0 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032451
X-RAY DIFFRACTIONf_angle_d0.823338
X-RAY DIFFRACTIONf_dihedral_angle_d10.9911447
X-RAY DIFFRACTIONf_chiral_restr0.046397
X-RAY DIFFRACTIONf_plane_restr0.004416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.365-3.44890.4766910.4551896X-RAY DIFFRACTION51
3.4489-3.54210.39951000.45971070X-RAY DIFFRACTION62
3.5421-3.64630.44411100.42061539X-RAY DIFFRACTION88
3.6463-3.76390.46091320.38611728X-RAY DIFFRACTION98
3.7639-3.89840.36831810.34251720X-RAY DIFFRACTION99
3.8984-4.05440.351310.32281721X-RAY DIFFRACTION99
4.0544-4.23870.34481390.30491739X-RAY DIFFRACTION99
4.2387-4.4620.29391750.26731716X-RAY DIFFRACTION99
4.462-4.74130.29641330.23811740X-RAY DIFFRACTION98
4.7413-5.10690.24741340.23711724X-RAY DIFFRACTION99
5.1069-5.61990.26281530.24131704X-RAY DIFFRACTION99
5.6199-6.43110.27111500.24781743X-RAY DIFFRACTION99
6.4311-8.09470.25231200.28011740X-RAY DIFFRACTION99
8.0947-44.8070.28651590.3121685X-RAY DIFFRACTION97

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