[English] 日本語
Yorodumi
- PDB-6ov2: Crystal structure of human claudin-9 in complex with Clostridium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ov2
TitleCrystal structure of human claudin-9 in complex with Clostridium perfringens entertoxin C-terminal domain in closed 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 / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / toxin activity / virus receptor activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity ...calcium-independent cell-cell adhesion / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / toxin activity / virus receptor activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Claudin-9 / 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-9 / 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
Claudin-9 / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7503
Polymers37,6582
Non-polymers921
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-13 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 111.570, 121.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.26 Å3/Da / Density % sol: 80.35 %
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

-
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: Aug 5, 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: 3.16→70 Å / Num. obs: 30828 / % possible obs: 96.4 % / Redundancy: 9.6 % / Biso Wilson estimate: 137.73 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.0408 / Net I/σ(I): 5.8
Reflection shellResolution: 3.16→3.24 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.18 / Num. unique obs: 2276 / CC1/2: 0.123 / Rrim(I) all: 6.589 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDS0.82data reduction
XSCALEJanuary 26, 2018data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model and PDB entry 3AM2

3am2


Resolution: 3.2→20.096 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.49
RfactorNum. reflection% reflection
Rfree0.2914 2362 8.04 %
Rwork0.2813 --
obs0.2821 29389 95.8 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 145.68 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 6 4 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032395
X-RAY DIFFRACTIONf_angle_d0.7693277
X-RAY DIFFRACTIONf_dihedral_angle_d6.321886
X-RAY DIFFRACTIONf_chiral_restr0.043399
X-RAY DIFFRACTIONf_plane_restr0.004402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.26510.59171290.54291504X-RAY DIFFRACTION90
3.2651-3.33580.50531320.50581640X-RAY DIFFRACTION99
3.3358-3.41310.45981330.4561659X-RAY DIFFRACTION100
3.4131-3.4980.431490.41611663X-RAY DIFFRACTION100
3.498-3.5920.43711510.40381665X-RAY DIFFRACTION99
3.592-3.69710.3514640.4037818X-RAY DIFFRACTION49
3.6971-3.81570.40951380.35741652X-RAY DIFFRACTION100
3.8157-3.9510.481540.45611536X-RAY DIFFRACTION93
3.951-4.1080.30921480.291649X-RAY DIFFRACTION100
4.108-4.29320.30181280.25071665X-RAY DIFFRACTION100
4.2932-4.51710.25031630.20881631X-RAY DIFFRACTION100
4.5171-4.79650.21311340.20491680X-RAY DIFFRACTION100
4.7965-5.1610.26091590.20271643X-RAY DIFFRACTION100
5.161-5.66980.2231490.22231633X-RAY DIFFRACTION100
5.6698-6.46620.2741330.24421695X-RAY DIFFRACTION100
6.4662-8.05840.26141440.27711642X-RAY DIFFRACTION100
8.0584-20.0960.26021540.27291652X-RAY DIFFRACTION100

+
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://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