[English] 日本語
Yorodumi
- PDB-4ons: Structural and thermodynamic characterization of cadherin-beta-ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ons
TitleStructural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation
Components
  • Catenin alpha-2
  • Catenin beta-1
KeywordsCELL ADHESION / four helix bundles
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / metanephros morphogenesis / lung cell differentiation / lung induction / epicardium-derived cardiac vascular smooth muscle cell differentiation / positive regulation of branching involved in lung morphogenesis / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation ...radial glia guided migration of Purkinje cell / metanephros morphogenesis / lung cell differentiation / lung induction / epicardium-derived cardiac vascular smooth muscle cell differentiation / positive regulation of branching involved in lung morphogenesis / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchyme morphogenesis / establishment of blood-retinal barrier / genitalia morphogenesis / RUNX3 regulates WNT signaling / neural plate development / regulation of secondary heart field cardioblast proliferation / cardiac vascular smooth muscle cell differentiation / glial cell fate determination / Regulation of CDH11 function / oviduct development / central nervous system vasculogenesis / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Schwann cell proliferation / trachea morphogenesis / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / regulation of synapse structural plasticity / positive regulation of epithelial cell proliferation involved in prostate gland development / Apoptotic cleavage of cell adhesion proteins / ectoderm development / proximal/distal pattern formation / endoderm formation / hair cycle process / establishment of blood-brain barrier / embryonic foregut morphogenesis / lens morphogenesis in camera-type eye / extrinsic component of postsynaptic membrane / Disassembly of the destruction complex and recruitment of AXIN to the membrane / embryonic axis specification / regulation of epithelial cell differentiation / positive regulation of epithelial cell differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / epithelial cell differentiation involved in prostate gland development / Formation of the beta-catenin:TCF transactivating complex / dorsal/ventral axis specification / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / oocyte development / epithelial tube branching involved in lung morphogenesis / positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / gastrulation with mouth forming second / embryonic skeletal limb joint morphogenesis / astrocyte-dopaminergic neuron signaling / VEGFR2 mediated vascular permeability / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / endodermal cell fate commitment / negative regulation of mitotic cell cycle, embryonic / TCF dependent signaling in response to WNT / Adherens junctions interactions / regulation of centriole-centriole cohesion / positive regulation of fibroblast growth factor receptor signaling pathway / morphogenesis of embryonic epithelium / layer formation in cerebral cortex / regulation of centromeric sister chromatid cohesion / Deactivation of the beta-catenin transactivating complex / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / animal organ development / positive regulation of endothelial cell differentiation / trachea formation / embryonic hindlimb morphogenesis / mesenchyme development / Ca2+ pathway / fungiform papilla formation / positive regulation of determination of dorsal identity / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / extrinsic component of presynaptic membrane / positive regulation of skeletal muscle tissue development / anterior/posterior axis specification / embryonic forelimb morphogenesis / synaptic vesicle clustering / male genitalia development / RHO GTPases activate IQGAPs / Regulation of CDH1 Function / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / dorsal root ganglion development / ventricular compact myocardium morphogenesis / endothelial tube morphogenesis / hindbrain development / delta-catenin binding / tissue homeostasis / modification of postsynaptic actin cytoskeleton / mesenchymal to epithelial transition / cranial skeletal system development / sympathetic ganglion development
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2780 / Alpha-catenin / Alpha-catenin/vinculin-like / Beta-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2780 / Alpha-catenin / Alpha-catenin/vinculin-like / Beta-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Catenin alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsPokutta, S. / Choi, H.-J. / Ahlsen, G. / Hansen, S.D. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Thermodynamic Characterization of Cadherin beta-Catenin alpha-Catenin Complex Formation.
Authors: Pokutta, S. / Choi, H.J. / Ahlsen, G. / Hansen, S.D. / Weis, W.I.
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catenin alpha-2
B: Catenin beta-1
C: Catenin alpha-2
D: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)74,5294
Polymers74,5294
Non-polymers00
Water39622
1
A: Catenin alpha-2
B: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)37,2642
Polymers37,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-32 kcal/mol
Surface area14900 Å2
MethodPISA
2
C: Catenin alpha-2
D: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)37,2642
Polymers37,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-34 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.125, 96.125, 65.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Catenin alpha-2 / Alpha N-catenin


Mass: 27351.385 Da / Num. of mol.: 2 / Fragment: beta-catenin binding domain, UNP residues 18-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna2, Catna2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61301
#2: Protein Catenin beta-1 / Beta-catenin


Mass: 9912.957 Da / Num. of mol.: 2 / Fragment: alpha-catenin binding domain, UNP residues 78-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.794→38.753 Å / Num. all: 16165 / Num. obs: 16165 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 60.42 Å2 / Rsym value: 0.068 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.79-2.953.30.4960.30.496193.1
2.95-3.123.20.272.50.27196.5
3.12-3.343.50.1913.50.191199.2
3.34-3.613.30.1255.20.125198.7
3.61-3.952.90.160.1193.3
3.95-4.423.30.05810.50.058198.4
4.42-5.13.10.048130.048195.1
5.1-6.253.30.04513.10.045197.9
6.25-8.843.30.03116.50.031194.1
8.84-38.7533.30.02817.60.028194.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.753 Å / SU ML: 0.45 / σ(F): 1.98 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1146 7.11 %
Rwork0.2033 --
obs0.2075 16123 96.67 %
all-17269 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 0 22 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034335
X-RAY DIFFRACTIONf_angle_d0.5765829
X-RAY DIFFRACTIONf_dihedral_angle_d11.5881655
X-RAY DIFFRACTIONf_chiral_restr0.021686
X-RAY DIFFRACTIONf_plane_restr0.002759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.92760.35321530.28591873X-RAY DIFFRACTION96
2.9276-3.08190.3561320.25161875X-RAY DIFFRACTION96
3.0819-3.27490.29291630.24511873X-RAY DIFFRACTION98
3.2749-3.52760.30541600.21861936X-RAY DIFFRACTION99
3.5276-3.88230.26591240.19861811X-RAY DIFFRACTION93
3.8823-4.44330.23571650.17571854X-RAY DIFFRACTION98
4.4433-5.59540.25281210.191905X-RAY DIFFRACTION96
5.5954-38.75680.22161280.18851850X-RAY DIFFRACTION96
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)
15.5589-1.53390.12444.7523-0.19473.5612-0.0658-0.13530.23340.40240.2419-0.1090.17690.4206-0.09180.2834-0.1411-0.00350.5262-0.09740.419316.4683-28.622323.8499
22.7116-0.699-0.37251.7536-0.34751.85030.1343-0.1947-0.3302-0.0950.1380.12840.9759-0.5111-0.07570.2745-0.2033-0.0580.49310.04060.28125.0813-38.262820.3278
33.0656-2.4284-3.48541.87572.62813.6952-0.2723-0.1469-0.85840.38190.2377-0.17980.35980.34210.08810.36730.09710.15350.646-0.11730.73634.8131-44.7665-3.6731
43.3623-1.1754-1.68211.145-0.18591.54820.58580.57570.52-0.1326-0.3531-0.2242-0.1668-0.272-0.18620.41910.04250.09870.8552-0.11820.649740.2691-39.0101-8.2952
56.288-0.0038-0.73022.84960.16963.60790.0592-0.39370.78830.02840.3975-0.5537-0.88350.4216-0.22740.3864-0.06770.12340.3809-0.10830.4620.1037-26.2213.0565
62.61770.5564-1.55470.7887-0.53882.4212-0.07230.0690.2106-0.11890.33060.07520.1352-0.3435-0.20230.2791-0.0403-0.05350.54340.13170.30488.6884-30.994710.5513
73.50820.70280.87624.4042-1.06984.5984-0.19030.41740.3381-0.63580.3913-0.355-0.1633-0.8982-0.04250.454-0.10480.11650.51130.01230.296917.768-29.1166-29.0231
81.9875-0.7381-0.05032.40530.12722.88410.0579-0.1384-0.1398-0.09050.16140.24120.9852-0.6209-0.08830.5247-0.1236-0.02950.39050.0160.300513.0267-43.3444-25.3396
93.8817-2.6972-4.58641.82773.17045.3498-0.0896-0.269-0.04330.0284-0.36960.8347-0.0704-0.72510.21110.58310.17290.15870.8898-0.01730.6362-3.2139-17.4253-1.6727
104.2024-0.3378-1.3282.16110.36012.75030.4322-1.02560.01430.0786-0.3344-0.2879-0.1449-0.4098-0.04851.18220.0840.20860.9392-0.15161.12642.1049-17.79456.4781
11-0.0184-0.0547-0.0344-0.037-0.052-0.0338-0.2734-0.4470.2280.1632-0.24720.2357-0.4818-0.60090.05061.8422-0.00860.59791.1727-0.38761.56750.0501-6.66919.828
120.2650.0403-0.5939-0.0049-0.11791.1152-0.23920.0072-0.02010.1382-0.1955-0.3339-0.22890.1348-0.00570.990.00360.34410.69340.12711.3843-0.7373-4.61290.5213
135.6536-1.45480.08745.20930.22783.4229-0.2813-0.12450.93210.37960.6684-1.2452-0.83770.8434-0.1350.3954-0.11080.0050.3991-0.18520.514320.2677-24.6466-16.7155
141.7243-0.5048-1.17383.12241.23933.59960.0513-0.06480.2046-0.01220.2002-0.16820.32550.4213-0.17970.41440.0476-0.14280.3325-0.01730.325618.6961-37.64-15.9897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 18:39
2X-RAY DIFFRACTION2chain A and resid 52:147
3X-RAY DIFFRACTION3chain A and resid 148:166
4X-RAY DIFFRACTION4chain A and resid 168:260
5X-RAY DIFFRACTION5chain B and resid 83:103
6X-RAY DIFFRACTION6chain B and resid 109:143
7X-RAY DIFFRACTION7chain C and resid 19:38
8X-RAY DIFFRACTION8chain C and resid 53:147
9X-RAY DIFFRACTION9chain C and resid 148:165
10X-RAY DIFFRACTION10chain C and resid 168:195
11X-RAY DIFFRACTION11chain C and resid 207:228
12X-RAY DIFFRACTION12chain C and resid 237:258
13X-RAY DIFFRACTION13chain D and resid 84:108
14X-RAY DIFFRACTION14chain D and resid 109:144

+
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