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- PDB-4k1n: Crystal structure of full-length mouse alphaE-catenin -

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Basic information

Entry
Database: PDB / ID: 4k1n
TitleCrystal structure of full-length mouse alphaE-catenin
ComponentsCatenin alpha-1
KeywordsCELL ADHESION / four-helix bundle / beta-catenin / F-actin
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / Adherens junctions interactions / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / 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 / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / 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 / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intercalated disc / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / cell motility / integrin-mediated signaling pathway / adherens junction / protein localization / cell-cell adhesion / beta-catenin binding / response to estrogen / male gonad development / cell migration / actin filament binding / cell-cell junction / actin cytoskeleton / cell junction / lamellipodium / regulation of cell population proliferation / cadherin binding / intracellular membrane-bounded organelle / 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: 6.5 Å
AuthorsIshiyama, N. / Ikura, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: An autoinhibited structure of alpha-catenin and its implications for vinculin recruitment to adherens junctions.
Authors: Ishiyama, N. / Tanaka, N. / Abe, K. / Yang, Y.J. / Abbas, Y.M. / Umitsu, M. / Nagar, B. / Bueler, S.A. / Rubinstein, J.L. / Takeichi, M. / Ikura, M.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)201,6242
Polymers201,6242
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-22 kcal/mol
Surface area53460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.684, 144.684, 136.757
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: 100812.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catna1, Ctnna1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / 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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M Sodium Citrate, 20% (w/v) PEG-3350, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 6.5→50 Å / Num. obs: 6581 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.128 / Χ2: 1.044 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
6.5-6.615.50.5213280.9331100
6.61-6.735.40.4523310.9321100
6.73-6.865.40.4313221.0781100
6.86-75.40.3583511.1041100
7-7.155.40.3123011.0861100
7.15-7.325.40.273471.0361100
7.32-7.55.40.2273341.0651100
7.5-7.75.40.1943221.0881100
7.7-7.935.40.1743231.0851100
7.93-8.185.30.1743331.1531100
8.18-8.475.30.153301.0391100
8.47-8.815.30.1463441.0991100
8.81-9.215.20.1313301.0741100
9.21-9.695.10.1293171.0711100
9.69-10.35.20.1273260.9551100
10.3-11.085.10.1243471.0671100
11.08-12.184.70.123221.02199.4
12.18-13.914.40.1173281.0091100
13.91-17.44.70.13230.988199.4
17.4-504.40.0933220.968195

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOV and 1ST6

1dov

1st6


Resolution: 6.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 643 10.2 %random
Rwork0.2243 ---
obs-5942 94.6 %-
Solvent computationBsol: 333.391 Å2
Displacement parametersBiso max: 354.92 Å2 / Biso mean: 354.92 Å2 / Biso min: 354.92 Å2
Baniso -1Baniso -2Baniso -3
1--26.901 Å20 Å20 Å2
2---26.901 Å20 Å2
3---53.801 Å2
Refinement stepCycle: LAST / Resolution: 6.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 0 0 8020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.5-6.730.3877580.375545251086
6.73-70.496600.382652858888.4
7-7.320.3571610.348350056192.4
7.32-7.70.3147590.278954460393.3
7.7-8.180.3234730.242652059394.7
8.18-8.810.2375670.182853259997.7
8.81-9.690.1974610.188358064198.3
9.69-11.080.1649630.157255962298.7
11.08-13.910.1796700.17753960999.2
13.91-500.3168710.294954561696.6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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