[English] 日本語
Yorodumi
- PDB-6cg6: mouse cadherin-10 EC1-2 adhesive fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cg6
Titlemouse cadherin-10 EC1-2 adhesive fragment
ComponentsCadherin-10
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / postsynaptic specialization membrane / homophilic cell adhesion via plasma membrane adhesion molecules / GABA-ergic synapse ...Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / postsynaptic specialization membrane / homophilic cell adhesion via plasma membrane adhesion molecules / GABA-ergic synapse / presynaptic active zone membrane / adherens junction / cell morphogenesis / beta-catenin binding / cell migration / cadherin binding / glutamatergic synapse / calcium ion binding / synapse
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å
AuthorsBrasch, J. / Harrison, O.J. / Shapiro, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM062270 United States
National Science Foundation (NSF, United States)MCB- 0918535 United States
CitationJournal: Cell Rep / Year: 2018
Title: Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior.
Authors: Brasch, J. / Katsamba, P.S. / Harrison, O.J. / Ahlsen, G. / Troyanovsky, R.B. / Indra, I. / Kaczynska, A. / Kaeser, B. / Troyanovsky, S. / Honig, B. / Shapiro, L.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4936
Polymers23,1481
Non-polymers3465
Water46826
1
A: Cadherin-10
hetero molecules

A: Cadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98612
Polymers46,2952
Non-polymers69110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3160 Å2
ΔGint-42 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.524, 87.524, 67.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Cadherin-10 / T2-cadherin


Mass: 23147.639 Da / Num. of mol.: 1 / Fragment: EC1-2 (UNP residues 55-261)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh10 / Production host: Escherichia coli (E. coli) / References: UniProt: P70408
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% v/v 2-propanol, 0.1 M MES, pH 6.0, 0.2 M calcium acetate, cryoprotectant: 30% v/v ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 7545 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.041 / Num. unique obs: 732

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CGU

6cgu


Resolution: 2.707→19.735 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2833 376 4.98 %
Rwork0.2377 --
obs0.2401 7545 99.87 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.707→19.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 18 26 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021679
X-RAY DIFFRACTIONf_angle_d0.5022277
X-RAY DIFFRACTIONf_dihedral_angle_d14.81005
X-RAY DIFFRACTIONf_chiral_restr0.046250
X-RAY DIFFRACTIONf_plane_restr0.003300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7067-3.09710.42341220.32342328X-RAY DIFFRACTION100
3.0971-3.89710.32611240.25752357X-RAY DIFFRACTION100
3.8971-19.73570.23361300.20772484X-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