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- PDB-6akg: Crystal structure of mouse claudin-3 P134G mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 6akg
TitleCrystal structure of mouse claudin-3 P134G mutant in complex with C-terminal fragment of Clostridium perfringens enterotoxin
Components
  • Claudin-3
  • Heat-labile enterotoxin B chain
KeywordsMEMBRANE PROTEIN/TOXIN / Cell adhesion / Tight junction / MEMBRANE PROTEIN-TOXIN complex
Function / homology
Function and homology information


cell junction maintenance / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / response to Gram-positive bacterium / regulation of transepithelial transport / regulation of membrane permeability / negative regulation of wound healing / positive regulation of bicellular tight junction assembly / epithelial cell morphogenesis / bicellular tight junction assembly ...cell junction maintenance / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / response to Gram-positive bacterium / regulation of transepithelial transport / regulation of membrane permeability / negative regulation of wound healing / positive regulation of bicellular tight junction assembly / epithelial cell morphogenesis / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / lateral plasma membrane / bicellular tight junction / negative regulation of cell migration / cell-cell junction / toxin activity / actin cytoskeleton organization / response to ethanol / cell adhesion / response to hypoxia / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / structural molecule activity / protein-containing complex / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Claudin-3 / 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
Heat-labile enterotoxin B chain / Claudin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Clostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsNakamura, S. / Irie, K. / Fujiyoshi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Nat Commun / Year: 2019
Title: Morphologic determinant of tight junctions revealed by claudin-3 structures.
Authors: Nakamura, S. / Irie, K. / Tanaka, H. / Nishikawa, K. / Suzuki, H. / Saitoh, Y. / Tamura, A. / Tsukita, S. / Fujiyoshi, Y.
History
DepositionAug 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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-3
B: Heat-labile enterotoxin B chain
C: Claudin-3
D: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)66,3934
Polymers66,3934
Non-polymers00
Water00
1
A: Claudin-3
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,1962
Polymers33,1962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-9 kcal/mol
Surface area14950 Å2
MethodPISA
2
C: Claudin-3
D: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,1962
Polymers33,1962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-12 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.710, 68.210, 107.880
Angle α, β, γ (deg.)90.000, 98.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Claudin-3


Mass: 19866.439 Da / Num. of mol.: 2 / Fragment: UNP residues 1-183 / Mutation: P134A,C103A, C106A, C181A, C182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cldn3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Z0G9
#2: Protein Heat-labile enterotoxin B chain


Mass: 13329.830 Da / Num. of mol.: 2 / Fragment: UNP residues 203-319 / Mutation: S313A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Production host: Escherichia coli (E. coli) / References: UniProt: P01558
Sequence detailsAUTHORS STATE THAT THE N-TERMINAL RESIDUES GHMASGS IN A AND C CHAINS ARE DERIVED FROM THE TEV ...AUTHORS STATE THAT THE N-TERMINAL RESIDUES GHMASGS IN A AND C CHAINS ARE DERIVED FROM THE TEV PROTEASE CLEAVAGE SITE AND LINKER AND THAT GLY201 AND SER202 IN B AND D CHAINS ARE DERIVED FROM THE THROMBIN CLEAVAGE SITE.

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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: 5.13 Å3/Da / Density % sol: 76.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8 / Details: HEPES, Magnesium nitrate, PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.3→49.34 Å / Num. obs: 9133 / % possible obs: 88.85 % / Redundancy: 6.7 % / Biso Wilson estimate: 214.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03868 / Rpim(I) all: 0.01638 / Rrim(I) all: 0.04212 / Net I/σ(I): 14.82
Reflection shellResolution: 4.3→4.49 Å / Redundancy: 7 % / Rmerge(I) obs: 1.817 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 490 / CC1/2: 0.689 / Rpim(I) all: 0.7385 / Rrim(I) all: 1.965 / % possible all: 53.84

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AKF

6akf


Resolution: 4.3→49.34 Å / SU ML: 0.8235 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 52.4904
RfactorNum. reflection% reflection
Rfree0.3278 413 5.05 %
Rwork0.2827 --
obs0.2848 8178 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 271.26 Å2
Refinement stepCycle: LAST / Resolution: 4.3→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 0 0 4482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01444570
X-RAY DIFFRACTIONf_angle_d1.73336243
X-RAY DIFFRACTIONf_chiral_restr0.0818758
X-RAY DIFFRACTIONf_plane_restr0.0069771
X-RAY DIFFRACTIONf_dihedral_angle_d15.36781551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.50.4045260.306609X-RAY DIFFRACTION55.27
4.5-4.730.3092330.2433773X-RAY DIFFRACTION71.01
4.73-5.030.3757530.2849938X-RAY DIFFRACTION88.25
5.03-5.420.4311480.30411093X-RAY DIFFRACTION99.65
5.42-5.960.3593730.28281054X-RAY DIFFRACTION99.21
5.96-6.820.3556610.25671086X-RAY DIFFRACTION99.57
6.82-8.590.2685560.21551095X-RAY DIFFRACTION99.05
8.59-49.340.3128630.30751117X-RAY DIFFRACTION98.66

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