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- PDB-5b2g: Crystal structure of human claudin-4 in complex with C-terminal f... -

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Basic information

Entry
Database: PDB / ID: 5b2g
TitleCrystal structure of human claudin-4 in complex with C-terminal fragment of Clostridium perfringens enterotoxin
Components
  • Endolysin,Claudin-4
  • Heat-labile enterotoxin B chain
KeywordsMEMBRANE PROTEIN / Complex / Cell-free protein expression system
Function / homology
Function and homology information


paracellular transport / positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / regulation of cell morphogenesis / tight junction / positive regulation of wound healing / chloride channel activity ...paracellular transport / positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / regulation of cell morphogenesis / tight junction / positive regulation of wound healing / chloride channel activity / renal absorption / chloride channel complex / lateral plasma membrane / bicellular tight junction / establishment of skin barrier / viral release from host cell by cytolysis / peptidoglycan catabolic process / basal plasma membrane / response to progesterone / female pregnancy / circadian rhythm / transmembrane signaling receptor activity / cell wall macromolecule catabolic process / cell-cell junction / lysozyme / lysozyme activity / toxin activity / host cell cytoplasm / cell adhesion / defense response to bacterium / positive regulation of cell migration / apical plasma membrane / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Jelly Rolls - #1050 / Claudin-4 / Claudin / Claudin, conserved site / Claudin family signature. / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Endolysin T4 type ...Jelly Rolls - #1050 / Claudin-4 / Claudin / Claudin, conserved site / Claudin family signature. / Clostridium enterotoxin / Clostridium enterotoxin / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Claudin-4 / Endolysin / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Clostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsShinoda, T. / Kimura-Someya, T. / Shirouzu, M. / Yokoyama, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Target Proteins Research Program Japan
Platform for Drug Discovery, Information, and Structural Life Science Japan
Grant-in-Aid for Young Scientists (B)25840028 Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for disruption of claudin assembly in tight junctions by an enterotoxin
Authors: Shinoda, T. / Shinya, N. / Ito, K. / Ohsawa, N. / Terada, T. / Hirata, K. / Kawano, Y. / Yamamoto, M. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M.
History
DepositionJan 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Source and taxonomy
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin,Claudin-4
B: Heat-labile enterotoxin B chain
C: Endolysin,Claudin-4
D: Heat-labile enterotoxin B chain
E: Endolysin,Claudin-4
F: Heat-labile enterotoxin B chain
G: Endolysin,Claudin-4
H: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)221,1618
Polymers221,1618
Non-polymers00
Water00
1
A: Endolysin,Claudin-4
B: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-10 kcal/mol
Surface area24870 Å2
MethodPISA
2
C: Endolysin,Claudin-4
D: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-8 kcal/mol
Surface area24080 Å2
MethodPISA
3
E: Endolysin,Claudin-4
F: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-9 kcal/mol
Surface area25700 Å2
MethodPISA
4
G: Endolysin,Claudin-4
H: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-11 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.920, 105.920, 244.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Endolysin,Claudin-4 / Lysis protein / Lysozyme / Muramidase / Clostridium perfringens enterotoxin receptor / CPE-receptor ...Lysis protein / Lysozyme / Muramidase / Clostridium perfringens enterotoxin receptor / CPE-receptor / Williams-Beuren syndrome chromosomal region 8 protein


Mass: 39410.793 Da / Num. of mol.: 4 / Fragment: UNP residues 2-162,UNP residues 1-183 / Mutation: R1012G, C1054T, C1097A, I1137R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: CLDN4, CPER, CPETR1, WBSCR8
Details (production host): Sample was prepared by the E.coli cell-free protein synthesis system
Production host: Escherichia coli (E. coli) / References: UniProt: P00720, UniProt: O14493, lysozyme
#2: Protein
Heat-labile enterotoxin B chain


Mass: 15879.505 Da / Num. of mol.: 4 / Fragment: UNP residues 187-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe
Details (production host): Sample was prepared by the E.coli cell-free protein synthesis system
Production host: Escherichia coli (E. coli) / References: UniProt: P01558
Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 63.07 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 75mM MES-NaOH, 20% PEG3350, 7-10% 1,6-hexanediol, 0.002% NaN3, 0.0005% 2,6-di-t-butyl-p-cresol, 150mM NaCl
PH range: 5.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 76023 / % possible obs: 99.6 % / Redundancy: 4.56 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 6.63

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AM2

3am2


Resolution: 3.5→48.589 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 34.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3087 1686 5 %
Rwork0.2881 --
obs0.2892 38500 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→48.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14200 0 0 0 14200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514453
X-RAY DIFFRACTIONf_angle_d1.17219596
X-RAY DIFFRACTIONf_dihedral_angle_d11.0018592
X-RAY DIFFRACTIONf_chiral_restr0.0562279
X-RAY DIFFRACTIONf_plane_restr0.0032451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.60310.42011410.37192667X-RAY DIFFRACTION100
3.6031-3.71930.38061400.34212659X-RAY DIFFRACTION100
3.7193-3.85220.34571410.30872692X-RAY DIFFRACTION100
3.8522-4.00640.33061390.30142643X-RAY DIFFRACTION100
4.0064-4.18860.33971420.30262685X-RAY DIFFRACTION100
4.1886-4.40930.33221410.27172690X-RAY DIFFRACTION100
4.4093-4.68540.29541400.25612649X-RAY DIFFRACTION100
4.6854-5.04680.28621420.26542694X-RAY DIFFRACTION100
5.0468-5.5540.30741400.28052675X-RAY DIFFRACTION100
5.554-6.35620.31211400.29812654X-RAY DIFFRACTION100
6.3562-8.00230.30271420.29862698X-RAY DIFFRACTION100
8.0023-48.59370.26071380.27172646X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 40.7097 Å / Origin y: -12.0877 Å / Origin z: -5.8343 Å
111213212223313233
T0.6668 Å2-0.1375 Å2-0.0211 Å2-0.5246 Å20.0034 Å2--0.6044 Å2
L0.8428 °2-0.1101 °20.1304 °2-0.3249 °2-0.0666 °2--0.5833 °2
S0.0254 Å °0.0607 Å °0.1672 Å °-0.0199 Å °0.0345 Å °-0.1502 Å °-0.1774 Å °0.0948 Å °-0.0672 Å °
Refinement TLS groupSelection details: all

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