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- PDB-1dov: CRYSTAL STRUCTURE OF THE ALPHA-CATENIN DIMERIZATION DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1dov
TitleCRYSTAL STRUCTURE OF THE ALPHA-CATENIN DIMERIZATION DOMAIN
ComponentsALPHA-CATENINAlpha catenin
KeywordsCELL ADHESION / four-helix bundle
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 / vinculin binding / cellular response to indole-3-methanol ...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 / vinculin binding / cellular response to indole-3-methanol / 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 / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / cell junction / regulation of cell population proliferation / cadherin binding / intracellular membrane-bounded organelle / apoptotic process / protein-containing complex binding / structural molecule activity / negative regulation of apoptotic process / identical protein binding / plasma membrane
Similarity search - Function
Alpha-catenin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsPokutta, S. / Weis, W.I.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure of the dimerization and beta-catenin-binding region of alpha-catenin.
Authors: Pokutta, S. / Weis, W.I.
History
DepositionDec 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ALPHA-CATENIN


Theoretical massNumber of molelcules
Total (without water)19,8761
Polymers19,8761
Non-polymers00
Water0
1
A: ALPHA-CATENIN

A: ALPHA-CATENIN


Theoretical massNumber of molelcules
Total (without water)39,7522
Polymers39,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area19170 Å2
MethodPISA
2
A: ALPHA-CATENIN

A: ALPHA-CATENIN


Theoretical massNumber of molelcules
Total (without water)39,7522
Polymers39,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)136.460, 136.460, 118.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a dimer. The twofold axis of the dimer is coincident with a crystallographic twofold. The dimer can by generated by application of the following rotation matrix: (-0.5 0.866 0.0) (0.866 0.5 0.0) (0.0 0.0 -1.0) and the translation vector (0. 0. 118.17)

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Components

#1: Protein ALPHA-CATENIN / Alpha catenin


Mass: 19875.953 Da / Num. of mol.: 1 / Fragment: DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: PEG 400, Tris, urea, dithiothreitol, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-40 mg/mlprotein1drop
2200 mMTris-HCl1reservoir
3900 mMurea1reservoir
427 %PEG4001reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 33971 / Num. obs: 8574 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.322 / Num. unique all: 5031 / % possible all: 100
Reflection
*PLUS
Num. measured all: 33971
Reflection shell
*PLUS
% possible obs: 100 % / Num. measured obs: 5031 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
DMmodel building
CNS0.5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
DMphasing
RefinementResolution: 3→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2593339.74 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.263 907 10.6 %RANDOM
Rwork0.218 ---
obs0.218 8574 99.3 %-
all-8574 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.52 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 69.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.57 Å216.46 Å20 Å2
2--10.57 Å20 Å2
3----21.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 0 1389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d14.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 80 9.3 %
Rwork0.323 778 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7667
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 66.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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