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- PDB-4e17: Alpha-E-catenin is an autoinhibited molecule that co-activates vi... -

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Basic information

Entry
Database: PDB / ID: 4.0E+17
TitleAlpha-E-catenin is an autoinhibited molecule that co-activates vinculin
Components
  • Catenin alpha-1
  • Vinculin
KeywordsCELL ADHESION / four helix bundle
Function / homology
Function and homology information


muscle tendon junction / negative regulation of integrin-mediated signaling pathway / Platelet degranulation / Smooth Muscle Contraction / VEGFR2 mediated vascular permeability / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web ...muscle tendon junction / negative regulation of integrin-mediated signaling pathway / Platelet degranulation / Smooth Muscle Contraction / VEGFR2 mediated vascular permeability / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / RHO GTPases activate IQGAPs / Adherens junctions interactions / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / gamma-catenin binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / fascia adherens / negative regulation of cell motility / cell-cell contact zone / Myogenesis / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / axon extension / protein localization to cell surface / negative regulation of protein localization to nucleus / lamellipodium assembly / axon regeneration / negative regulation of neuroblast proliferation / regulation of focal adhesion assembly / smoothened signaling pathway / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / alpha-actinin binding / brush border / skeletal muscle myofibril / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intercalated disc / stress fiber / regulation of cell migration / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / cell projection / cell motility / Neutrophil degranulation / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / protein localization / cell-cell adhesion / Z disc / 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 / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / structural molecule activity / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alpha-catenin / Vinculin repeated domain signature. / Vinculin / 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) ...Alpha-catenin / Vinculin repeated domain signature. / Vinculin / 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
Vinculin / Catenin alpha-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsChoi, H.-J. / Pokutta, S. / Cadwell, G.W. / Bankston, L.A. / Liddington, R.C. / Weis, W.I.
CitationJournal: To be Published
Title: Conformational plasticity of alpha-catenin revealed by binding interactions with vinculin
Authors: Choi, H.-J. / Pokutta, S. / Bankston, L. / Liddington, R. / Weis, W.I.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Vinculin
B: Catenin alpha-1


Theoretical massNumber of molelcules
Total (without water)33,7842
Polymers33,7842
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-27 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.747, 55.969, 128.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vinculin /


Mass: 29379.932 Da / Num. of mol.: 1 / Fragment: D1 domain (UNP residues 1-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide Catenin alpha-1 / / Alpha E-catenin / 102 kDa cadherin-associated protein / CAP102


Mass: 4403.830 Da / Num. of mol.: 1 / Fragment: vinculin binding domain (UNP residues 321-356)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna1, Catna1 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26231
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG8000, 100 mM MES, pH 6.8, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 16376 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Χ2: 1.684 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.40.5627761.079195.8
2.34-2.383.50.4747931.092197.8
2.38-2.433.50.4018441.065199.1
2.43-2.483.60.3457681.188198.3
2.48-2.533.50.3498421.212199.1
2.53-2.593.60.2947871.358198.9
2.59-2.663.50.2528381.338198.7
2.66-2.733.60.2137991.275198.8
2.73-2.813.50.198341.381199.2
2.81-2.93.60.1558041.495198.2
2.9-33.50.1438131.511197.8
3-3.123.60.1098201.636198.3
3.12-3.263.60.1018101.707197.9
3.26-3.443.60.0878171.952197.3
3.44-3.653.60.078102.548197.4
3.65-3.933.60.0618352.672197.3
3.93-4.333.60.0488192.529197.2
4.33-4.953.50.0418402.383197.7
4.95-6.243.50.0428612.005197.5
6.24-503.30.0368662.058191.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T01

1t01


Resolution: 2.304→42.133 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8356 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1267 7.76 %RANDOM
Rwork0.2161 ---
obs0.218 16336 97.59 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.345 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 149.53 Å2 / Biso mean: 50.4 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.8476 Å20 Å2-0 Å2
2--6.3762 Å2-0 Å2
3----5.5286 Å2
Refinement stepCycle: LAST / Resolution: 2.304→42.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 0 51 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032198
X-RAY DIFFRACTIONf_angle_d0.7392974
X-RAY DIFFRACTIONf_chiral_restr0.048364
X-RAY DIFFRACTIONf_plane_restr0.003379
X-RAY DIFFRACTIONf_dihedral_angle_d13.075853
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 (%)
2.304-2.39670.29031360.26961590172696
2.3967-2.50570.27511700.24571644181499
2.5057-2.63780.27911300.2241667179799
2.6378-2.80310.25521620.22881673183599
2.8031-3.01940.24991300.21291664179498
3.0194-3.32320.27471360.21641684182098
3.3232-3.80380.22691380.20051675181398
3.8038-4.79130.20591170.18211725184297
4.7913-42.14020.2251480.24291747189595
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.02060.0595-0.02680.0722-0.01770.02960.12710.13240.00760.1244-0.05430.01660.0389-0.00170.1732-0.03280.04010.1083-0.04440.1313-0.7019-8.643323.797
2-0-0.00340.00070.0044-0.00150.00050.0164-0.01380.0428-0.00710.01450.002-0.00540.00130.19050.0520.00680.1248-0.04070.1814-0.1563-0.68746.9574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 254
2X-RAY DIFFRACTION2chain BB326 - 353

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