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- PDB-6o3e: mouse aE-catenin 82-883 -

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Basic information

Entry
Database: PDB / ID: 6o3e
Titlemouse aE-catenin 82-883
ComponentsCatenin alpha-1
KeywordsCELL ADHESION / catenin / actin binding
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / Adherens junctions interactions / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding ...negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / Adherens junctions interactions / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding / flotillin complex / negative regulation of cell motility / Myogenesis / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / integrin-mediated signaling pathway / cell motility / adherens junction / protein localization / beta-catenin binding / cell-cell adhesion / response to estrogen / male gonad development / cell-cell junction / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / regulation of cell population proliferation / cadherin binding / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / identical protein binding / plasma membrane
Similarity search - Function
Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.001 Å
AuthorsPokutta, S. / Weis, W.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114462 United States
CitationJournal: Sci Rep / Year: 2019
Title: Binding partner- and force-promoted changes in alpha E-catenin conformation probed by native cysteine labeling.
Authors: Terekhova, K. / Pokutta, S. / Kee, Y.S. / Li, J. / Tajkhorshid, E. / Fuller, G. / Dunn, A.R. / Weis, W.I.
History
DepositionFeb 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catenin alpha-1
B: Catenin alpha-1


Theoretical massNumber of molelcules
Total (without water)178,1372
Polymers178,1372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area52510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.262, 145.262, 136.269
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Catenin alpha-1 / 102 kDa cadherin-associated protein / Alpha E-catenin / CAP102


Mass: 89068.391 Da / Num. of mol.: 2 / Mutation: C116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna1, Catna1 / Production host: Escherichia coli (E. coli) / References: UniProt: P26231

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM Tris, pH 8.5, 60 mM lithium sulfate, 23.5 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4→19.971 Å / Num. obs: 26524 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.095 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4-4.283.51.2448740.5630.7751.46998.8
11.31-19.973.20.0299620.9980.0180.03580.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGG

4igg


Resolution: 4.001→19.971 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / Phase error: 34.3
RfactorNum. reflection% reflection
Rfree0.2429 1324 5.02 %
Rwork0.2135 --
obs0.215 25046 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 595.41 Å2 / Biso mean: 209.1052 Å2 / Biso min: 64.98 Å2
Refinement stepCycle: final / Resolution: 4.001→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 0 0 8070
Num. residues----1077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0005-4.15930.38251390.37632800293998
4.1593-4.34680.37271450.35412745289097
4.3468-4.57330.36391450.33742724286996
4.5733-4.8560.31181300.2792882301299
4.856-5.22470.32371660.25682772293899
5.2247-5.73920.35741520.31122753290598
5.7392-6.54390.32111440.28552775291998
6.5439-8.15030.22611500.19512814296499
8.1503-19.97080.15061530.12332773292698

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