[English] 日本語
Yorodumi
- PDB-5b2g: Crystal structure of human claudin-4 in complex with C-terminal f... -

+
Open data


ID or keywords:

Loading...

-
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


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 / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity ...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 / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / renal absorption / chloride channel activity / 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-cell junction / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / toxin activity / host cell cytoplasm / cell adhesion / positive regulation of cell migration / defense response to bacterium / apical plasma membrane / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-4 / 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 / Endolysin T4 type ...Claudin-4 / 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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more