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- PDB-4k1o: Crystal structure of the alphaN-catenin actin-binding domain -

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Basic information

Entry
Database: PDB / ID: 4k1o
TitleCrystal structure of the alphaN-catenin actin-binding domain
ComponentsCatenin alpha-2
KeywordsCELL ADHESION / five-helix bundle / F-actin / alpha-catenin
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / presynaptic active zone cytoplasmic component / Myogenesis / regulation of neuron migration / brain morphogenesis ...radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / presynaptic active zone cytoplasmic component / Myogenesis / regulation of neuron migration / brain morphogenesis / dendrite morphogenesis / regulation of neuron projection development / parallel fiber to Purkinje cell synapse / prepulse inhibition / postsynaptic density, intracellular component / axonogenesis / hippocampal mossy fiber to CA3 synapse / adherens junction / cell-cell adhesion / actin filament binding / lamellipodium / actin cytoskeleton / basolateral plasma membrane / postsynaptic density / cadherin binding / axon / structural molecule activity / identical protein binding / nucleus / cytoplasm
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 / SAD / Resolution: 2.603 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3914
Polymers29,1031
Non-polymers2883
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catenin alpha-2
hetero molecules

A: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7828
Polymers58,2052
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2340 Å2
ΔGint-80 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.152, 112.152, 56.316
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

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


Mass: 29102.627 Da / Num. of mol.: 1 / Fragment: C-terminal actin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catna2, Ctnna2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: Q61301
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE ALPHA N-CATANIN ISOFORM I, UNIPROT ENTRY CODE Q61301-2

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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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97911
SYNCHROTRONAPS 19-ID20.97915
Detector
TypeIDDetectorDate
ADSC Q2101CCDAug 15, 2011
ADSC Q2102CCDAug 15, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979151
ReflectionResolution: 2.6→50 Å / Num. all: 12400 / Num. obs: 12361 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 70.6 Å2 / Rsym value: 0.049 / Χ2: 1.08 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.646.30.5196050.9821,2100
2.64-2.697.20.4376211.3051,2100
2.69-2.747.80.3456110.9711,2100
2.74-2.88.20.266270.9431,2100
2.8-2.869.10.2245971.0121,2100
2.86-2.939.50.216331.0131,2100
2.93-39.60.1526011.1061,2100
3-3.089.50.1376271.1011,2100
3.08-3.179.50.1166081.1181,2100
3.17-3.289.50.0926301.0961,2100
3.28-3.399.50.0676181.1051,2100
3.39-3.539.30.0676171.2791,2100
3.53-3.699.40.0556241.1691,2100
3.69-3.889.50.0496211.2181,299.8
3.88-4.139.40.0416261.0921,299.8
4.13-4.459.50.0366100.981,299.5
4.45-4.899.50.0346210.9861,299.8
4.89-5.69.30.0336470.9691,299.7
5.6-7.059.30.0346271.0421,299.7
7.05-508.40.0316291.1051,295.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.603→39.736 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7918 / SU ML: 0.26 / σ(F): 0 / Phase error: 27.25 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1202 10.11 %Random
Rwork0.1946 ---
obs0.1982 11888 95.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.03 Å2 / Biso mean: 70.8448 Å2 / Biso min: 47.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.603→39.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 15 7 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081552
X-RAY DIFFRACTIONf_angle_d1.1042093
X-RAY DIFFRACTIONf_chiral_restr0.075245
X-RAY DIFFRACTIONf_plane_restr0.004263
X-RAY DIFFRACTIONf_dihedral_angle_d13.015583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6033-2.70750.34481100.28131001111181
2.7075-2.83070.29441250.26691115124090
2.8307-2.97990.32381310.26361161129293
2.9799-3.16650.29381320.25741185131795
3.1665-3.41090.31911360.24021218135499
3.4109-3.75390.26761400.1981250139099
3.7539-4.29650.19641370.17781236137399
4.2965-5.4110.18041440.160512501394100
5.411-39.74090.191470.16671270141798

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