[English] 日本語
Yorodumi
- PDB-3tt9: Crystal structure of the stable degradation fragment of human pla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tt9
TitleCrystal structure of the stable degradation fragment of human plakophilin 2 isoform a (PKP2a) C752R variant
ComponentsPlakophilin-2
KeywordsCELL ADHESION
Function / homology
Function and homology information


maintenance of protein localization at cell tip / maintenance of animal organ identity / intermediate filament bundle assembly / cell-cell signaling involved in cardiac conduction / intermediate filament binding / desmosome assembly / regulation of cell-substrate adhesion / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization ...maintenance of protein localization at cell tip / maintenance of animal organ identity / intermediate filament bundle assembly / cell-cell signaling involved in cardiac conduction / intermediate filament binding / desmosome assembly / regulation of cell-substrate adhesion / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / regulation of substrate adhesion-dependent cell spreading / cell tip / desmosome / Formation of the cornified envelope / alpha-catenin binding / cornified envelope / cell communication by electrical coupling involved in cardiac conduction / positive regulation of sodium ion transport / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle tissue morphogenesis / intermediate filament / regulation of heart rate by cardiac conduction / intercalated disc / sodium channel regulator activity / protein localization to plasma membrane / adherens junction / protein kinase C binding / cell-cell adhesion / cell-cell junction / cell junction / heart development / transmembrane transporter binding / molecular adaptor activity / cadherin binding / DNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Plakophilin/Delta catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchuetz, A. / Roske, Y. / Gerull, B. / Heinemann, U.
CitationJournal: Circ Cardiovasc Genet / Year: 2012
Title: Molecular insights into arrhythmogenic right ventricular cardiomyopathy caused by plakophilin-2 missense mutations.
Authors: Kirchner, F. / Schuetz, A. / Boldt, L.H. / Martens, K. / Dittmar, G. / Haverkamp, W. / Thierfelder, L. / Heinemann, U. / Gerull, B.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plakophilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3983
Polymers26,2141
Non-polymers1842
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.350, 63.038, 74.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Plakophilin-2


Mass: 26214.057 Da / Num. of mol.: 1 / Fragment: ARM domains 1, 2, and 3
Source method: isolated from a genetically manipulated source
Details: amino acids 346-817 expressed, stable fragment (aa 346-576) purified and crystallized
Source: (gene. exp.) Homo sapiens (human) / Gene: PKP2 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q99959
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR STATES THAT THEY CRYSTALLIZED ISOFORM A WHICH IS EQUIVALENT TO ISOFORM 1. THE SEQUENCE ...THE AUTHOR STATES THAT THEY CRYSTALLIZED ISOFORM A WHICH IS EQUIVALENT TO ISOFORM 1. THE SEQUENCE DATABASE REFERENCE CORRESPONDING TO THIS ISOFORM IS UNP Q99959-2.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir: 22% (w/v) PEG 3350, 75 M malonic acid pH 7.0, protein: 5 mg/mL in 20 mM HEPES, NaOH pH 7.5, 0.1 M NaCl, 3 mM DTT, mix 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 19, 2009
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.55→35 Å / Num. all: 32554 / Num. obs: 32363 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 2.87 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
MxCuBEGUIdata collection
PHASERphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XM9

1xm9


Resolution: 1.55→33.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.809 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19231 1619 5 %RANDOM
Rwork0.15822 ---
all0.15994 32554 --
obs0.15994 30744 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.662 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 12 282 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221942
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9772636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9225256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11524.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8981517
X-RAY DIFFRACTIONr_chiral_restr0.1270.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021463
X-RAY DIFFRACTIONr_mcbond_it0.9221.51193
X-RAY DIFFRACTIONr_mcangle_it1.58521931
X-RAY DIFFRACTIONr_scbond_it2.7543749
X-RAY DIFFRACTIONr_scangle_it4.4664.5693
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 115 -
Rwork0.202 2180 -
obs--100 %
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)
10.307-0.23820.15730.4219-0.28440.2190.01440.0174-0.0162-0.0155-0.015-0.0040.00610.0210.00060.0042-0.00130.0010.0059-0.00370.010515.349-3.51620.091
21.5614-1.273-0.20232.2771-1.53423.98580.09260.1813-0.1681-0.0313-0.00840.2080.0873-0.2427-0.08420.02610.0061-0.01210.0594-0.02220.0529-5.7563.701-1.071
30.69930.07730.12110.71450.03940.2781-0.0261-0.034-0.00720.00130.04450.0297-0.0207-0.0204-0.01840.00920.00410.00120.00630.00370.0098-4.3612.28112.956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A344 - 491
2X-RAY DIFFRACTION2A492 - 506
3X-RAY DIFFRACTION3A507 - 576

+
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