[English] 日本語
Yorodumi
- PDB-8hyi: Crystal structure of human P-cadherin MEC12 (X dimer) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hyi
TitleCrystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine
ComponentsCadherin-3
KeywordsCELL ADHESION / inhibitor
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 / catenin complex / Adherens junctions interactions ...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 / catenin complex / Adherens junctions interactions / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / adherens junction / cell morphogenesis / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / cell junction / cell migration / cell adhesion / cadherin binding / response to xenobiotic stimulus / 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-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine / Cadherin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSenoo, A. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05766 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101094 Japan
Japan Society for the Promotion of Science (JSPS)19J14451 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
Japan Society for the Promotion of Science (JSPS)18H05425 Japan
Japan Society for the Promotion of Science (JSPS)20H02531 Japan
Japan Society for the Promotion of Science (JSPS)16H02420 Japan
CitationJournal: Protein Sci. / Year: 2023
Title: Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion.
Authors: Senoo, A. / Nagatoishi, S. / Kuroda, D. / Ito, S. / Ueno, G. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)47,74112
Polymers46,8442
Non-polymers89710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-42 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 99.498, 107.568
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-22R / 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine


Mass: 250.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.075M HEPES sodium pH 7.5, 1.125M Lithium sulfate monohydrate, 25% 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: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→47.31 Å / Num. obs: 20527 / % possible obs: 99.9 % / Redundancy: 7.329 % / Biso Wilson estimate: 57.946 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.252 / Rrim(I) all: 0.271 / Χ2: 0.8 / Net I/σ(I): 9.7 / Num. measured all: 150449
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
2.85-3.037.4172.1681.0423926323732260.5452.33199.7
3.03-3.247.4481.22.0322842306930670.7241.28999.9
3.24-3.497.420.6533.721296287128700.8750.702100
3.49-3.827.4010.3436.8619599264926480.9630.369100
3.82-4.277.360.20111.2717685240324030.9840.216100
4.27-4.937.3320.11817.415706214221420.9960.127100
4.93-6.027.2510.12716.1813291183318330.9940.137100
6.02-8.447.0870.0920.9110333145814580.9970.097100
8.44-47.316.5580.03541.14577188688010.03899.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.18 Å47.31 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zmq

4zmq


Resolution: 2.85→47.31 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 1062 5.18 %
Rwork0.2196 19454 -
obs0.2223 20516 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.61 Å2 / Biso mean: 66.1267 Å2 / Biso min: 16.77 Å2
Refinement stepCycle: final / Resolution: 2.85→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 94 0 3376
Biso mean--113.25 --
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.980.39441180.35112387250599
2.98-3.140.34991260.306123822508100
3.14-3.340.33061210.275324292550100
3.34-3.60.32621390.235223762515100
3.6-3.960.25371360.200524252561100
3.96-4.530.24621430.17924222565100
4.53-5.710.2311290.185524662595100
5.71-47.310.2531500.211725672717100

+
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