[English] 日本語
Yorodumi
- PDB-3oux: Structure of beta-catenin with phosphorylated Lef-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oux
TitleStructure of beta-catenin with phosphorylated Lef-1
Components
  • Catenin beta-1
  • Lymphoid enhancer-binding factor 1
KeywordsPROTEIN BINDING / Wnt/beta-catenin signaling pathway / TCF / Lef / transcription factors / phosphorylation
Function / homology
Function and homology information


Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling ...Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / 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 / negative regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of granulocyte differentiation / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins / negative regulation of interleukin-5 production / Disassembly of the destruction complex and recruitment of AXIN to the membrane / hair cycle process / negative regulation of interleukin-13 production / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / negative regulation of apoptotic process in bone marrow cell / endoderm formation / mesenchyme development / armadillo repeat domain binding / T-helper 1 cell differentiation / trachea morphogenesis / Formation of the beta-catenin:TCF transactivating complex / positive regulation of cell proliferation in bone marrow / 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 / negative regulation of striated muscle tissue development / 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 / formation of radial glial scaffolds / apoptotic process involved in morphogenesis / regulation of centriole-centriole cohesion / neutrophil differentiation / 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 / cell development / RHO GTPases activate IQGAPs / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / secondary palate development / beta-catenin-TCF complex / endodermal cell fate commitment / gamma-catenin binding / acinar cell differentiation / positive regulation of gamma-delta T cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / apoptotic process involved in blood vessel morphogenesis / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / T cell receptor V(D)J recombination / 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
Similarity search - Function
TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / Beta-catenin / Catenin binding domain superfamily / HMG (high mobility group) box / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat ...TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / Beta-catenin / Catenin binding domain superfamily / HMG (high mobility group) box / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Few Secondary Structures / Irregular / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Lymphoid enhancer-binding factor 1 / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWeis, W.I. / Sun, J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Biochemical and structural characterization of beta-catenin interactions with nonphosphorylated and CK2-phosphorylated Lef-1.
Authors: Sun, J. / Weis, W.I.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Dec 9, 2015Group: Other
Revision 1.4Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catenin beta-1
B: Lymphoid enhancer-binding factor 1


Theoretical massNumber of molelcules
Total (without water)66,0092
Polymers66,0092
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-13 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.56, 115.56, 195.93
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-51-

HOH

21A-62-

HOH

-
Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 58988.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#2: Protein Lymphoid enhancer-binding factor 1 / LEF-1


Mass: 7020.700 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lef1, Lef-1 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / References: UniProt: P27782
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: well solution: 7% PEG 3000, 100 mM sodium citrate. protein solution: 100 micro-M beta-cat-arm, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4→99.5 Å / Num. obs: 26264 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M1E

1m1e


Resolution: 2.4→37.11 Å / SU ML: 0.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1530 5.83 %
Rwork0.199 --
obs-26264 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.936 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5587 Å2-0 Å20 Å2
2---9.5587 Å2-0 Å2
3---19.1175 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 0 97 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084124
X-RAY DIFFRACTIONf_angle_d1.0715604
X-RAY DIFFRACTIONf_dihedral_angle_d14.7861499
X-RAY DIFFRACTIONf_chiral_restr0.07686
X-RAY DIFFRACTIONf_plane_restr0.005725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.30691170.24482203X-RAY DIFFRACTION99
2.4775-2.5660.29521520.21842202X-RAY DIFFRACTION100
2.566-2.66870.29681330.21612206X-RAY DIFFRACTION100
2.6687-2.79010.30381440.21672210X-RAY DIFFRACTION100
2.7901-2.93720.34651390.22262231X-RAY DIFFRACTION100
2.9372-3.12110.3131420.21482235X-RAY DIFFRACTION100
3.1211-3.36190.28271470.22042232X-RAY DIFFRACTION100
3.3619-3.70.28031440.19652244X-RAY DIFFRACTION100
3.7-4.23470.22711160.16822290X-RAY DIFFRACTION100
4.2347-5.33280.22541430.17122296X-RAY DIFFRACTION100
5.3328-37.11490.21091530.18352385X-RAY DIFFRACTION99
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)
10.8534-0.7944-0.22181.81810.56590.1775-0.2405-0.23540.01091.34820.34290.0771-0.31270.2872-0.04122.0828-0.20820.17260.56360.0190.251132.36432.144345.7312
20.22280.1645-0.07310.4288-0.04170.2978-0.02940.0389-0.22730.0996-0.0448-0.0147-0.03830.01660.06360.0895-0.00810.01060.0718-0.03940.21538.1135-23.424-5.2077
30.11140.16570.10570.29150.21170.17140.06080.0584-0.07490.03090.1796-0.57930.05670.079-0.23010.15050.0347-0.16280.1601-0.17420.694142.653-22.7032-0.3098
40.1471-0.3810.0361.0315-0.25240.6768-0.0345-0.0197-0.027-0.2626-0.11470.1142-0.88650.17040.14051.3027-0.2708-0.27220.4868-0.04970.483741.17924.207626.8813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 151:236)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 237:665)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 11:42)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 45:60)

+
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