[English] 日本語
Yorodumi
- PDB-7cme: Crystal structure of human P-cadherin MEC12 (X dimer) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cme
TitleCrystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor)
ComponentsCadherin-3
KeywordsCELL ADHESION / inhibitor / complex
Function / homology
Function and homology information


negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex / retina homeostasis / cell-cell junction assembly / adherens junction organization / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / positive regulation of canonical Wnt signaling pathway / cell junction / cell adhesion / response to xenobiotic stimulus / cadherin binding / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine / Cadherin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSenoo, A. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K.
CitationJournal: Commun Biol / Year: 2021
Title: Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion
Authors: Senoo, A. / Ito, S. / Nagatoishi, S. / Saito, Y. / Ueno, G. / Kuroda, D. / Yoshida, K. / Tashima, T. / Kudo, S. / Sando, S. / Tsumoto, K.
History
DepositionJul 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadherin-3
B: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86713
Polymers46,8442
Non-polymers1,02311
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-42 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.828, 99.113, 107.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cadherin-3 / Placental cadherin / P-cadherin


Mass: 23422.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Production host: Escherichia coli (E. coli) / References: UniProt: P22223
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-G60 / 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine


Mass: 208.687 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13ClN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17M Sodium acetate trihydrate, 0.085M TRIS pH 8.5, w/v 25.5% PEG 4000, 15% v/v Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→45.04 Å / Num. obs: 31971 / % possible obs: 99.9 % / Redundancy: 7.38 % / Biso Wilson estimate: 68.736 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.076 / Χ2: 0.862 / Net I/σ(I): 19.21 / Num. measured all: 235947
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.67.4661.5581.337762507050580.5381.67499.8
2.6-2.787.5180.8292.5235997479047880.8340.89100
2.78-37.5070.3855.2233497446244620.9620.414100
3-3.297.4890.16511.6130990413841380.9920.177100
3.29-3.677.4360.0822.3827876374937490.9980.086100
3.67-4.247.3060.04637.2624328333033300.9990.05100
4.24-5.187.2020.03447.0520541285228520.9990.036100
5.18-7.287.1040.03546.4116006225322530.9990.038100
7.28-45.046.6740.02257.8489501349134110.02499.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.19 Å45.04 Å

-
Processing

Software
NameVersionClassification
PHENIX1.17refinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zmq

4zmq


Resolution: 2.45→45.04 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1647 5.15 %
Rwork0.2087 30317 -
obs0.2107 31964 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.93 Å2 / Biso mean: 76.5952 Å2 / Biso min: 38.39 Å2
Refinement stepCycle: final / Resolution: 2.45→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 107 29 3416
Biso mean--121.66 59.52 -
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.45-2.530.35711380.339124622600
2.53-2.610.34621550.318424762631
2.61-2.70.39151360.308724772613
2.7-2.810.32571450.288524742619
2.81-2.940.36231350.274625142649
2.94-3.090.29221360.248725062642
3.09-3.290.31571400.238324982638
3.29-3.540.29751400.237525242664
3.54-3.890.2561370.196725182655
3.89-4.460.19151090.1825922701
4.46-5.610.17911360.168325682704
5.61-45.040.21771400.181527082848

+
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