[English] 日本語
Yorodumi
- PDB-2bct: THE ARMADILLO REPEAT REGION FROM MURINE BETA-CATENIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bct
TitleTHE ARMADILLO REPEAT REGION FROM MURINE BETA-CATENIN
ComponentsBETA-CATENIN
KeywordsSTRUCTURAL PROTEIN / ARMADILLO REPEAT / BETA-CATENIN
Function / homology
Function and homology information


lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins / Disassembly of the destruction complex and recruitment of AXIN to the membrane ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins / Disassembly of the destruction complex and recruitment of AXIN to the membrane / hair cycle process / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / endoderm formation / mesenchyme development / trachea morphogenesis / Formation of the beta-catenin:TCF transactivating complex / positive regulation of epithelial cell differentiation / Deactivation of the beta-catenin transactivating complex / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / animal organ development / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / VEGFR2 mediated vascular permeability / regulation of epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / Degradation of beta-catenin by the destruction complex / Adherens junctions interactions / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / mesenchymal cell proliferation / alpha-catenin binding / cranial skeletal system development / regulation of calcium ion import / cell projection membrane / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell differentiation involved in prostate gland development
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuber, A.H. / Nelson, W.J. / Weis, W.I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Three-dimensional structure of the armadillo repeat region of beta-catenin.
Authors: Huber, A.H. / Nelson, W.J. / Weis, W.I.
History
DepositionJul 30, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-CATENIN


Theoretical massNumber of molelcules
Total (without water)56,3141
Polymers56,3141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.090, 75.590, 134.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BETA-CATENIN


Mass: 56314.336 Da / Num. of mol.: 1 / Fragment: ARMADILLO REPEAT REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5
Details: 10% (W/V) PEG 8000, 875 MM NACL, 200 MM TRIS-HCL, PH 8.5
Crystal grow
*PLUS
pH: 10.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlbeta-591drop
210 mMCAPS1drop
350 mM1dropNaCl
41 mMDTT1drop
510 %(w/v)PEG80001reservoir
6200 mMTris-HCl1reservoir
7875 mM1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 11818 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 22.7
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.257 / % possible all: 93.4
Reflection shell
*PLUS
% possible obs: 93.4 %

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BCT

3bct


Resolution: 2.9→40 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1178 10.4 %RANDOM
Rwork0.211 ---
obs0.211 11380 94 %-
Solvent computationSolvent model: X-PLOR/CNS / Bsol: 15.23 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--4.05 Å20 Å2
3----7.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 0 0 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it4.682
X-RAY DIFFRACTIONc_scbond_it4.642
X-RAY DIFFRACTIONc_scangle_it6.752.5
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 182 10.8 %
Rwork0.365 1507 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2

+
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