[English] 日本語
Yorodumi
- PDB-4zmx: Crystal structure of human P-cadherin (int-X-dimer) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zmx
TitleCrystal structure of human P-cadherin (int-X-dimer)
ComponentsCadherin-3
KeywordsCELL ADHESION / classical cadherin P-cadherin cell-adhesion dimerization conformational change
Function / homology
Function and homology information


: / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex ...: / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly / retina homeostasis / Adherens junctions interactions / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell-cell adhesion / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / cell morphogenesis / cell junction / positive regulation of canonical Wnt signaling pathway / cell migration / cell adhesion / 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 / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCaaveiro, J.M.M. / Kudo, S. / Tsumoto, K.
CitationJournal: Structure / Year: 2016
Title: Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism
Authors: Kudo, S. / Caaveiro, J.M. / Tsumoto, K.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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-3
B: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5928
Polymers46,3512
Non-polymers2406
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-34 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.460, 181.460, 40.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

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


Mass: 23175.682 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320 / Mutation: W2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: Champion pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22223
#2: Chemical
ChemComp-CA / CALCIUM ION


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 4,000 10% 2-isopropanol HEPES 100 mM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→43.59 Å / Num. obs: 14283 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 3.4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMN

4zmn


Resolution: 3.1→43.59 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.884 / SU B: 34.94 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23538 717 5 %RANDOM
Rwork0.20608 ---
obs0.20755 13559 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.368 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 3.1→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 6 0 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193154
X-RAY DIFFRACTIONr_bond_other_d0.0010.022937
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9594291
X-RAY DIFFRACTIONr_angle_other_deg0.65336819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26225.683139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50215516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8851511
X-RAY DIFFRACTIONr_chiral_restr0.0530.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6193.0051604
X-RAY DIFFRACTIONr_mcbond_other0.6193.0041603
X-RAY DIFFRACTIONr_mcangle_it1.1324.5071999
X-RAY DIFFRACTIONr_mcangle_other1.1314.5072000
X-RAY DIFFRACTIONr_scbond_it0.4773.0851550
X-RAY DIFFRACTIONr_scbond_other0.4773.0831547
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8844.5942289
X-RAY DIFFRACTIONr_long_range_B_refined2.80823.2753204
X-RAY DIFFRACTIONr_long_range_B_other2.80823.2793205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 51 -
Rwork0.274 971 -
obs--98.46 %
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)
13.653-0.3415-0.82531.51940.05241.74960.09110.4493-0.1755-0.1108-0.06770.50250.004-0.5155-0.02340.1411-0.0044-0.05840.1665-0.01370.172267.83520.1301-12.2104
21.2591-0.71450.54044.8059-1.49742.24810.0395-0.06120.05310.1632-0.01030.00990.0032-0.3619-0.02910.101-0.03850.02010.1476-0.03490.166759.31144.41154.5244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 213
2X-RAY DIFFRACTION2B5 - 213

+
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