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- PDB-6duw: Crystal structure of the alpha-N-catenin actin-binding domain H1 ... -

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Basic information

Entry
Database: PDB / ID: 6duw
TitleCrystal structure of the alpha-N-catenin actin-binding domain H1 mutant
ComponentsCatenin alpha-2CTNNA2
KeywordsCELL ADHESION / five-helix bundle / F-actin-binding / mechanosensor
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / brain morphogenesis / catenin complex / dendrite morphogenesis / regulation of neuron projection development / positive regulation of muscle cell differentiation / Myogenesis ...radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / brain morphogenesis / catenin complex / dendrite morphogenesis / regulation of neuron projection development / positive regulation of muscle cell differentiation / Myogenesis / prepulse inhibition / axonogenesis / adherens junction / structural constituent of cytoskeleton / beta-catenin binding / cell-cell adhesion / actin filament binding / cell migration / actin cytoskeleton / cadherin binding / axon / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha N-catenin / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Oct 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-2


Theoretical massNumber of molelcules
Total (without water)28,1201
Polymers28,1201
Non-polymers00
Water1,60389
1
A: Catenin alpha-2

A: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)56,2412
Polymers56,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2910 Å2
ΔGint-13 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.652, 108.652, 133.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1083-

HOH

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Components

#1: Protein Catenin alpha-2 / CTNNA2 / Alpha N-catenin / Alpha-catenin-related protein


Mass: 28120.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNA2, CAPR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26232
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate, 10 mM cobalt chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.08 Å / Num. obs: 24191 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 47.58 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K1O

4k1o


Resolution: 2.2→42.08 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4348
RfactorNum. reflection% reflection
Rfree0.2263 2413 10 %
Rwork0.2015 --
obs0.204 24141 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 0 89 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761492
X-RAY DIFFRACTIONf_angle_d0.7892014
X-RAY DIFFRACTIONf_chiral_restr0.049236
X-RAY DIFFRACTIONf_plane_restr0.0044257
X-RAY DIFFRACTIONf_dihedral_angle_d2.12631288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.27151380.24471244X-RAY DIFFRACTION97.81
2.24-2.290.29181390.23521248X-RAY DIFFRACTION100
2.29-2.350.26581400.22961252X-RAY DIFFRACTION100
2.35-2.40.25281390.24051250X-RAY DIFFRACTION100
2.4-2.470.25931390.22071260X-RAY DIFFRACTION100
2.47-2.540.28341400.22251264X-RAY DIFFRACTION100
2.54-2.620.2491380.20671241X-RAY DIFFRACTION100
2.62-2.720.27831430.22971289X-RAY DIFFRACTION100
2.72-2.830.24541400.22621251X-RAY DIFFRACTION100
2.83-2.960.2661410.23151273X-RAY DIFFRACTION100
2.96-3.110.25551420.23111282X-RAY DIFFRACTION99.93
3.11-3.310.24791430.21221273X-RAY DIFFRACTION100
3.31-3.560.21621410.21041278X-RAY DIFFRACTION100
3.56-3.920.20351450.17981306X-RAY DIFFRACTION100
3.92-4.490.16661440.16321298X-RAY DIFFRACTION100
4.49-5.650.22521490.18691339X-RAY DIFFRACTION100
5.65-42.090.21941520.19971380X-RAY DIFFRACTION96.6

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