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- PDB-6akf: Crystal structure of mouse claudin-3 P134A mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 6akf
TitleCrystal structure of mouse claudin-3 P134A 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 / negative regulation of phosphate transmembrane transport / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion / response to Gram-positive bacterium / cell-cell junction maintenance / cell-cell adhesion mediator activity / regulation of membrane permeability / retinal pigment epithelium development / bicellular tight junction assembly ...cell junction maintenance / negative regulation of phosphate transmembrane transport / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion / response to Gram-positive bacterium / cell-cell junction maintenance / cell-cell adhesion mediator activity / regulation of membrane permeability / retinal pigment epithelium development / bicellular tight junction assembly / apicolateral plasma membrane / regulation of transepithelial transport / epithelial cell morphogenesis / regulation of cell morphogenesis / tight junction / 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 / 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: 3.9 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 6, 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
C: Claudin-3
E: Claudin-3
G: Claudin-3
B: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
F: Heat-labile enterotoxin B chain
H: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)132,8418
Polymers132,8418
Non-polymers00
Water00
1
A: Claudin-3
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2102
Polymers33,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-8 kcal/mol
Surface area14460 Å2
MethodPISA
2
C: Claudin-3
D: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2102
Polymers33,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-11 kcal/mol
Surface area14570 Å2
MethodPISA
3
E: Claudin-3
F: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2102
Polymers33,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-10 kcal/mol
Surface area14720 Å2
MethodPISA
4
G: Claudin-3
H: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)33,2102
Polymers33,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 127.450, 165.700
Angle α, β, γ (deg.)90.000, 104.530, 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: 19880.467 Da / Num. of mol.: 4 / 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.: 4 / 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: 5.57 Å3/Da / Density % sol: 77.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: HEPES, Sodium acetate, Magnesium nitrate, PEG 3350

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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: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→46.66 Å / Num. obs: 25301 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 95.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09076 / Rpim(I) all: 0.05924 / Rrim(I) all: 0.1089 / Net I/σ(I): 8.17
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2529 / CC1/2: 0.575 / Rpim(I) all: 0.682 / Rrim(I) all: 1.244 / % possible all: 99.49

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Processing

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

6ake


Resolution: 3.9→46.66 Å / SU ML: 0.6606 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.9559
RfactorNum. reflection% reflection
Rfree0.312 1314 5.2 %
Rwork0.2737 --
obs0.2758 25284 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 119.35 Å2
Refinement stepCycle: LAST / Resolution: 3.9→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8888 0 0 0 8888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01159059
X-RAY DIFFRACTIONf_angle_d1.593412357
X-RAY DIFFRACTIONf_chiral_restr0.08271490
X-RAY DIFFRACTIONf_plane_restr0.00591525
X-RAY DIFFRACTIONf_dihedral_angle_d15.43413104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.060.37171360.35522670X-RAY DIFFRACTION99.43
4.06-4.240.3311580.31152631X-RAY DIFFRACTION98.69
4.24-4.460.32161370.27622654X-RAY DIFFRACTION98.76
4.46-4.740.28351490.23712656X-RAY DIFFRACTION98.42
4.74-5.110.30421350.23932656X-RAY DIFFRACTION98.52
5.11-5.620.31371580.23952670X-RAY DIFFRACTION99.26
5.62-6.430.3391410.23052664X-RAY DIFFRACTION98.42
6.43-8.10.25651490.21882678X-RAY DIFFRACTION98.47
8.1-48.170.31651510.31462691X-RAY DIFFRACTION97.33

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