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- PDB-4p79: Crystal structure of mouse claudin-15 -

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Basic information

Entry
Database: PDB / ID: 4p79
TitleCrystal structure of mouse claudin-15
ComponentsClaudin-15
KeywordsCELL ADHESION / tight junction / membrane protein / paracellular channel
Function / homology
Function and homology information


calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / bicellular tight junction assembly / lateral plasma membrane / bicellular tight junction / monoatomic ion transport / membrane => GO:0016020 / cell adhesion / structural molecule activity / identical protein binding / plasma membrane
Similarity search - Function
Claudin-15 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / Claudin / Claudin, conserved site / Claudin family signature. / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Claudin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsSuzuki, H. / Nishizawa, T. / Tani, K. / Yamazaki, Y. / Tamura, A. / Ishitani, R. / Dohmae, N. / Tsukita, S. / Nureki, O. / Fujiyoshi, Y.
CitationJournal: Science / Year: 2014
Title: Crystal structure of a claudin provides insight into the architecture of tight junctions.
Authors: Suzuki, H. / Nishizawa, T. / Tani, K. / Yamazaki, Y. / Tamura, A. / Ishitani, R. / Dohmae, N. / Tsukita, S. / Nureki, O. / Fujiyoshi, Y.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Derived calculations
Revision 1.2Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Claudin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1583
Polymers21,4451
Non-polymers7132
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.250, 28.403, 58.587
Angle α, β, γ (deg.)90.000, 100.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Claudin-15


Mass: 21444.658 Da / Num. of mol.: 1 / Fragment: TM region / Mutation: C102A, C183A, C184A, and 185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cldn15 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Z0S5
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 30% PEG400, 10 mM HEPES-NaOH, 2 mM 2-mercaptoethanol
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 8, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→38.265 Å / Num. obs: 14967 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.243 / Χ2: 1.014 / Net I/σ(I): 7.92 / Num. measured all: 113916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.460.5311.8131.337131111610971.97198.3
2.46-2.530.6371.6951.648687113411341.818100
2.53-2.60.8171.2062.278381108510861.293100
2.6-2.680.8321.1622.267928102710231.24599.6
2.68-2.770.8280.8993.047783101410130.96499.9
2.77-2.860.9210.6983.6277079979980.747100
2.86-2.970.90.6344.0969608958990.679100
2.97-3.090.9390.5474.4572199359330.58699.8
3.09-3.230.9620.4625.2168968918880.49599.7
3.23-3.390.9730.3296.7963158188160.35399.8
3.39-3.570.9850.2249.5861527957930.2499.7
3.57-3.790.9890.17911.6856197307300.192100
3.79-4.050.9920.12814.9555177137170.137100
4.05-4.370.9960.09916.9444386406010.10693.9
4.37-4.790.9970.08519.725066153380.09155
4.79-5.360.9970.08520.6141725445400.09199.3
5.36-6.190.9940.10119.236724734750.108100
6.19-7.580.9970.07421.4931324054040.0899.8
7.58-10.720.9970.05827.0324403163150.06299.7
10.720.9970.04828.0312611731670.05196.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.3_1479)refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→38.265 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 1495 10.03 %
Rwork0.2209 13416 -
obs0.2242 14911 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.19 Å2 / Biso mean: 46.3018 Å2 / Biso min: 27.82 Å2
Refinement stepCycle: final / Resolution: 2.4→38.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 42 21 1391
Biso mean--51.84 43.8 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021399
X-RAY DIFFRACTIONf_angle_d0.4871890
X-RAY DIFFRACTIONf_chiral_restr0.019221
X-RAY DIFFRACTIONf_plane_restr0.002227
X-RAY DIFFRACTIONf_dihedral_angle_d10.664470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47750.33831330.32411207134099
2.4775-2.5660.30231420.278612761418100
2.566-2.66870.3251340.259112351369100
2.6687-2.79010.28131390.246912591398100
2.7901-2.93720.28581400.215612451385100
2.9372-3.12110.35081410.22212601401100
3.1211-3.3620.22181380.224512071345100
3.362-3.70010.22141420.189712661408100
3.7001-4.23490.22191400.194412421382100
4.2349-5.33320.25531100.2101963107377
5.3332-38.27010.21581360.220712561392100

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