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- PDB-6dv1: Crystal structure of the alpha-E-catenin actin-binding domain -

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Basic information

Entry
Database: PDB / ID: 6dv1
TitleCrystal structure of the alpha-E-catenin actin-binding domain
ComponentsCatenin alpha-1
KeywordsCELL ADHESION / five-helix bundle / F-actin-binding / mechanosensor
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 / 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
BROMIDE ION / Catenin alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsIshiyama, N. / Ikura, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2018
Title: Force-dependent allostery of the alpha-catenin actin-binding domain controls adherens junction dynamics and functions.
Authors: Ishiyama, N. / Sarpal, R. / Wood, M.N. / Barrick, S.K. / Nishikawa, T. / Hayashi, H. / Kobb, A.B. / Flozak, A.S. / Yemelyanov, A. / Fernandez-Gonzalez, R. / Yonemura, S. / Leckband, D.E. / ...Authors: Ishiyama, N. / Sarpal, R. / Wood, M.N. / Barrick, S.K. / Nishikawa, T. / Hayashi, H. / Kobb, A.B. / Flozak, A.S. / Yemelyanov, A. / Fernandez-Gonzalez, R. / Yonemura, S. / Leckband, D.E. / Gottardi, C.J. / Tepass, U. / Ikura, M.
History
DepositionJun 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,2529
Polymers57,6612
Non-polymers5927
Water1,74797
1
B: Catenin alpha-1
hetero molecules

A: Catenin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2529
Polymers57,6612
Non-polymers5927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area3320 Å2
ΔGint-34 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.292, 80.607, 104.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 28830.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna1, Catna1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26231
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


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

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium bromide, 2.2 M ammonium sulfate, 3% w/v D-galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0, 0.9198
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91981
ReflectionResolution: 2.2→46.15 Å / Num. obs: 24938 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Net I/σ(I): 31.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.15 Å / SU ML: 0.2668 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.3052
RfactorNum. reflection% reflection
Rfree0.2523 2264 9.32 %
Rwork0.2063 --
obs0.2106 24304 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 15 97 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812992
X-RAY DIFFRACTIONf_angle_d0.84244017
X-RAY DIFFRACTIONf_chiral_restr0.0476468
X-RAY DIFFRACTIONf_plane_restr0.0051508
X-RAY DIFFRACTIONf_dihedral_angle_d2.57612243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.36221290.27741246X-RAY DIFFRACTION89.11
2.24-2.30.33481340.24351256X-RAY DIFFRACTION92.79
2.3-2.350.2841400.22861329X-RAY DIFFRACTION94.41
2.35-2.420.27711350.23621310X-RAY DIFFRACTION95.7
2.42-2.490.27521390.22281353X-RAY DIFFRACTION96.44
2.49-2.570.29641360.21951369X-RAY DIFFRACTION97.79
2.57-2.660.28011400.22441375X-RAY DIFFRACTION97.99
2.66-2.770.30731420.23671357X-RAY DIFFRACTION98.49
2.77-2.890.25731450.2271408X-RAY DIFFRACTION99.04
2.89-3.050.28491390.22861372X-RAY DIFFRACTION99.34
3.05-3.240.27751440.21621404X-RAY DIFFRACTION99.55
3.24-3.490.24451470.21291435X-RAY DIFFRACTION99.94
3.49-3.840.21351440.19061412X-RAY DIFFRACTION99.94
3.84-4.390.21461460.17691431X-RAY DIFFRACTION100
4.39-5.530.2471480.18981452X-RAY DIFFRACTION99.94
5.53-46.160.23421560.20031531X-RAY DIFFRACTION99.65

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