[English] 日本語
Yorodumi
- PDB-3k6f: Crystal structure of mouse T-cadherin EC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k6f
TitleCrystal structure of mouse T-cadherin EC1
ComponentsT-cadherin
KeywordsCELL ADHESION / T-cadherin / Calcium / Cell membrane / Cleavage on pair of basic residues / Glycoprotein / GPI-anchor / Lipoprotein / Membrane
Function / homology
Function and homology information


low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / Adherens junctions interactions / localization within membrane / cell-cell adhesion mediated by cadherin / low-density lipoprotein particle binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion / catenin complex ...low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / Adherens junctions interactions / localization within membrane / cell-cell adhesion mediated by cadherin / low-density lipoprotein particle binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion / catenin complex / cell-cell junction assembly / adherens junction organization / sprouting angiogenesis / positive regulation of positive chemotaxis / lamellipodium assembly / positive regulation of cell-matrix adhesion / Rac protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / lipoprotein particle binding / Rho protein signal transduction / regulation of endocytosis / keratinocyte proliferation / endothelial cell migration / GABA-ergic synapse / positive regulation of calcium-mediated signaling / positive regulation of endothelial cell proliferation / caveola / adherens junction / positive regulation of smooth muscle cell proliferation / cell morphogenesis / neuron projection / positive regulation of cell migration / cadherin binding / negative regulation of cell population proliferation / external side of plasma membrane / synapse / calcium ion binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.813 Å
AuthorsShapiro, L. / Ciatto, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: T-cadherin structures reveal a novel adhesive binding mechanism
Authors: Ciatto, C. / Bahna, F. / Zampieri, N. / Vansteenhouse, H.C. / Katsamba, P.S. / Ahlsen, G. / Harrison, O.J. / Brasch, J. / Jin, X. / Posy, S. / Vendome, J. / Ranscht, B. / Jessell, T.M. / Honig, B. / Shapiro, L.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cadherin
B: T-cadherin


Theoretical massNumber of molelcules
Total (without water)21,8502
Polymers21,8502
Non-polymers00
Water3,657203
1
A: T-cadherin


Theoretical massNumber of molelcules
Total (without water)10,9251
Polymers10,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: T-cadherin


Theoretical massNumber of molelcules
Total (without water)10,9251
Polymers10,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.355, 50.355, 122.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-139-

HOH

21A-167-

HOH

31A-168-

HOH

41B-128-

HOH

51B-173-

HOH

61B-208-

HOH

-
Components

#1: Protein T-cadherin / / Truncated cadherin / Cadherin-13 / T-cad / Heart cadherin / H-cadherin


Mass: 10925.205 Da / Num. of mol.: 2 / Fragment: EC1 domain: UNP residues 140-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WTR5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Ammonium sulfate, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Vertical focusing mirror
RadiationMonochromator: Bent single Si(111) crystal (horizontal focusing and deflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 16137 / % possible obs: 99.3 % / Redundancy: 10.8 % / Biso Wilson estimate: 17.473 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.125 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRB entry 3K6D

3k6d


Resolution: 1.813→19.447 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.859 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.226 1584 10.01 %
Rwork0.168 --
obs0.168 15825 99.43 %
Solvent computationBsol: 63.705 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 77.38 Å2 / Biso mean: 22.144 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.404 Å2-0 Å2-0 Å2
2--2.404 Å20 Å2
3----4.809 Å2
Refinement stepCycle: LAST / Resolution: 1.813→19.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 203 1741
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.3611
X-RAY DIFFRACTIONf_bond_d0.0091
X-RAY DIFFRACTIONf_chiral_restr0.0881
X-RAY DIFFRACTIONf_dihedral_angle_d16.2151
X-RAY DIFFRACTIONf_plane_restr0.0071
X-RAY DIFFRACTIONf_nbd_refined4.1271
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.813-1.8360.151455X-RAY DIFFRACTION2883
1.836-1.8590.144538X-RAY DIFFRACTION2891
1.859-1.8830.152500X-RAY DIFFRACTION2891
1.883-1.9090.171515X-RAY DIFFRACTION2891
1.909-1.9360.154536X-RAY DIFFRACTION2890
1.936-1.9650.148487X-RAY DIFFRACTION2890
1.965-1.9960.143507X-RAY DIFFRACTION2889
1.996-2.0280.157528X-RAY DIFFRACTION2890
2.028-2.0630.159492X-RAY DIFFRACTION2891
2.063-2.1010.154516X-RAY DIFFRACTION2889
2.101-2.1410.167499X-RAY DIFFRACTION2890
2.141-2.1850.163531X-RAY DIFFRACTION2890
2.185-2.2320.159492X-RAY DIFFRACTION2889
2.232-2.2840.167518X-RAY DIFFRACTION2890
2.284-2.3410.168487X-RAY DIFFRACTION2889
2.341-2.4040.177534X-RAY DIFFRACTION2890
2.404-2.4750.175486X-RAY DIFFRACTION2890
2.475-2.5550.169531X-RAY DIFFRACTION2890
2.555-2.6460.18513X-RAY DIFFRACTION2889
2.646-2.7510.18496X-RAY DIFFRACTION2890
2.751-2.8760.187512X-RAY DIFFRACTION2890
2.876-3.0270.176510X-RAY DIFFRACTION2890
3.027-3.2160.169507X-RAY DIFFRACTION2890
3.216-3.4630.164513X-RAY DIFFRACTION2890
3.463-3.8090.148516X-RAY DIFFRACTION2889
3.809-4.3550.145508X-RAY DIFFRACTION2890
4.355-5.4670.149510X-RAY DIFFRACTION2888
5.467-19.4470.207504X-RAY DIFFRACTION2887
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.522-0.05480.40890.79370.29370.6508-0.06820.08120.01820.04910.0469-0.0329-0.01050.12410.02890.1164-0.0056-0.01350.13510.00280.0858-3.6365-17.2331-10.0523
21.40810.42590.81170.71390.10581.1558-0.10280.17810.0719-0.06590.01810.02810.00570.09830.07470.1328-0.0038-0.0250.07160.0110.06052.3298-22.6219.3758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 99
2X-RAY DIFFRACTION2chain BB0 - 99

+
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