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- PDB-6ov3: Crystal structure of human claudin-9 in complex with Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 6ov3
TitleCrystal structure of human claudin-9 in complex with Clostridium perfringens entertoxin C-terminal domain in open form
Components
  • Claudin-9
  • Heat-labile enterotoxin B chain
KeywordsCELL ADHESION / Claudin / Enterotoxin / Tight junction protein / Transmembrane protein
Function / homology
Function and homology information


calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / virus receptor activity / toxin activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity ...calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / virus receptor activity / toxin activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-9 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Jelly Rolls - #1050 / Claudin / Claudin, conserved site / Claudin family signature. / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily ...Claudin-9 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Jelly Rolls - #1050 / Claudin / Claudin, conserved site / Claudin family signature. / 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
Claudin-9 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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)R01GM024485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM103277 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Claudin-9 structures reveal mechanism for toxin-induced gut barrier breakdown.
Authors: Vecchio, A.J. / Stroud, R.M.
History
DepositionMay 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Claudin-9
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)37,6582
Polymers37,6582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.981, 114.817, 115.602
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-9


Mass: 22862.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLDN9 / Cell line (production host): Tn5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95484
#2: Protein Heat-labile enterotoxin B chain


Mass: 14795.565 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 194-319)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 6.12 Å3/Da / Density % sol: 79.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 150 mM sodium acetate, sodium cacodylate, Bis-Tris propane, pH 4.5, 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 S 6M / Detector: PIXEL / Date: Oct 20, 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: 3.2→70.98 Å / Num. obs: 16155 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 145.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.056 / Rrim(I) all: 0.139 / Net I/σ(I): 3.9
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 4.941 / Num. unique obs: 2877 / CC1/2: 0.512 / Rpim(I) all: 2.146 / Rrim(I) all: 5.397 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model and PDB entry 3AM2

3am2


Resolution: 3.25→20.125 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.59
RfactorNum. reflection% reflection
Rfree0.3077 2113 8.16 %
Rwork0.3007 --
obs0.3013 14613 90.48 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 185.27 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 0 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042292
X-RAY DIFFRACTIONf_angle_d0.9583149
X-RAY DIFFRACTIONf_dihedral_angle_d6.721764
X-RAY DIFFRACTIONf_chiral_restr0.048385
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2503-3.32560.5322740.5718871X-RAY DIFFRACTION49
3.3256-3.40840.54781110.53021246X-RAY DIFFRACTION71
3.4084-3.50010.50551350.52061460X-RAY DIFFRACTION84
3.5001-3.60250.55191540.5161622X-RAY DIFFRACTION92
3.6025-3.71810.55261070.49381207X-RAY DIFFRACTION69
3.7181-3.85010.45521530.41631695X-RAY DIFFRACTION98
3.8501-4.00310.43641560.38571730X-RAY DIFFRACTION99
4.0031-4.18380.33561480.33281785X-RAY DIFFRACTION100
4.1838-4.40220.31561600.28111721X-RAY DIFFRACTION99
4.4022-4.67470.23871510.25631752X-RAY DIFFRACTION99
4.6747-5.03040.3191490.24041753X-RAY DIFFRACTION100
5.0304-5.52710.30281450.26071712X-RAY DIFFRACTION98
5.5271-6.30530.27411550.26941740X-RAY DIFFRACTION99
6.3053-7.86440.35491420.28541765X-RAY DIFFRACTION100
7.8644-20.1250.22441730.261731X-RAY DIFFRACTION100

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