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- PDB-6ake: Crystal structure of mouse claudin-3 in complex with C-terminal f... -

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Basic information

Entry
Database: PDB / ID: 6ake
TitleCrystal structure of mouse claudin-3 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 membrane permeability / negative regulation of wound healing / regulation of transepithelial transport / epithelial cell morphogenesis / bicellular tight junction assembly / apicolateral plasma membrane ...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 membrane permeability / negative regulation of wound healing / regulation of transepithelial transport / epithelial cell morphogenesis / bicellular tight junction assembly / apicolateral plasma membrane / positive regulation of bicellular tight junction assembly / regulation of cell morphogenesis / tight junction / positive regulation of wound healing / bicellular tight junction / lateral plasma membrane / negative regulation of cell migration / cell-cell junction / actin cytoskeleton organization / toxin activity / response to ethanol / response to hypoxia / positive regulation of cell migration / 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 / Jelly Rolls - #1050 / Claudin / Claudin, conserved site / Claudin family signature. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily ...Claudin-3 / Jelly Rolls - #1050 / Claudin / Claudin, conserved site / Claudin family signature. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
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: 3.6 Å
AuthorsNakamura, S. / Irie, K. / Fujiyoshi, Y.
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 27, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)66,4734
Polymers66,4734
Non-polymers00
Water00
1
A: Claudin-3
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2362
Polymers33,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-11 kcal/mol
Surface area14700 Å2
MethodPISA
2
C: Claudin-3
D: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2362
Polymers33,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 66.630, 111.540
Angle α, β, γ (deg.)90.000, 97.550, 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 / Clostridium perfringens enterotoxin receptor 2 / CPE-receptor 2


Mass: 19906.504 Da / Num. of mol.: 2 / Fragment: UNP residues 1-183 / Mutation: C103A, C106A, C181A, C182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cldn3, Cpetr2 / 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
Has protein modificationY
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: 5.45 Å3/Da / Density % sol: 77.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: Tris-HCl, sodium chloride, magnesium nitrate, PEG 2000 MME, LMNG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→45.9 Å / Num. obs: 15888 / % possible obs: 93.92 % / Redundancy: 5 % / Biso Wilson estimate: 147.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.024 / Rrim(I) all: 0.054 / Net I/σ(I): 14.86
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 952 / CC1/2: 0.561 / Rpim(I) all: 0.58 / Rrim(I) all: 1.33 / % possible all: 60.68

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3x29

3x29


Resolution: 3.6→45.9 Å / SU ML: 0.6158 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.2082 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.283 756 5.05 %Random selection
Rwork0.2641 14212 --
obs0.2651 14968 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.66 Å2
Refinement stepCycle: LAST / Resolution: 3.6→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 0 0 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174391
X-RAY DIFFRACTIONf_angle_d1.56416002
X-RAY DIFFRACTIONf_chiral_restr0.0784731
X-RAY DIFFRACTIONf_plane_restr0.0056741
X-RAY DIFFRACTIONf_dihedral_angle_d16.37151482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.880.35271090.35512144X-RAY DIFFRACTION71.5
3.88-4.270.33981580.28362977X-RAY DIFFRACTION99.37
4.27-4.880.27871590.2192999X-RAY DIFFRACTION100
4.88-6.150.29551500.23963041X-RAY DIFFRACTION99.84
6.15-45.90.26131800.27593051X-RAY DIFFRACTION98.9

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