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- PDB-4e18: Alpha-E-catenin is an autoinhibited molecule that co-activates vi... -

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Basic information

Entry
Database: PDB / ID: 4.0E+18
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 / gamma-catenin binding / dystroglycan binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / cellular response to indole-3-methanol / vinculin binding / flotillin complex / fascia adherens / negative regulation of cell motility / cell-cell contact zone / Myogenesis / apical junction assembly / costamere / 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 / ovarian follicle development / regulation of cell migration / 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 / beta-catenin binding / Z disc / response to estrogen / male gonad development / cell migration / actin filament binding / cell-cell junction / actin cytoskeleton / cell junction / lamellipodium / 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 / negative regulation of apoptotic process / structural molecule activity / protein homodimerization activity / protein-containing complex / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2510 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2510 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / 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: 2.403 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)35,8112
Polymers35,8112
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-35 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.233, 68.102, 99.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

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


Mass: 6431.176 Da / Num. of mol.: 1 / Fragment: vinculin binding domain (UNP residues 302-356)
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.: 74 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG3350, 100 mM bis-tris-propane, pH 8.0, 100 mM sodium nitrate, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 2.4→50 Å / Num. obs: 14046 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.207 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.443.10.3196320.784187.5
2.44-2.493.30.2696130.771188.2
2.49-2.533.30.2936270.82191.3
2.53-2.593.30.2296770.852195.2
2.59-2.643.40.226820.858196.9
2.64-2.73.40.1957130.847199.3
2.7-2.773.50.187080.843199.6
2.77-2.853.60.1567120.8221100
2.85-2.933.60.1436961.018199.6
2.93-3.023.60.1297061.041100
3.02-3.133.60.1087191.2951100
3.13-3.263.60.097211.263199.9
3.26-3.413.60.0717101.24199.6
3.41-3.583.60.0577151.318199.9
3.58-3.813.60.0517151.44199.6
3.81-4.13.50.057291.637199.6
4.1-4.523.50.0517292.071199.3
4.52-5.173.40.0457231.752198.6
5.17-6.513.50.0437471.515199.1
6.51-503.20.0277721.554194.6

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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: 2.403→49.787 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7689 / SU ML: 0.34 / σ(F): 0 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 1050 7.49 %RANDOM
Rwork0.2177 ---
obs0.2217 14022 97.1 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.796 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 144.21 Å2 / Biso mean: 58.536 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--10.9579 Å20 Å2-0 Å2
2--22.9662 Å2-0 Å2
3----12.0083 Å2
Refinement stepCycle: LAST / Resolution: 2.403→49.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 74 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032327
X-RAY DIFFRACTIONf_angle_d0.6573142
X-RAY DIFFRACTIONf_chiral_restr0.039380
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d11.56899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.403-2.52920.31951260.25831646177287
2.5292-2.68770.32411520.24611795194796
2.6877-2.89520.31141440.239318682012100
2.8952-3.18650.30811780.242518582036100
3.1865-3.64750.26111560.221518952051100
3.6475-4.59490.2341460.181915206199
4.5949-49.79820.26381480.21821995214397
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5899-0.3742.89650.8102-1.23847.9592-0.0051-0.23830.0540.14470.01760.0409-0.0107-0.2871-0.01250.23730.02410.03160.2446-0.05670.3602-8.109412.2749-26.2125
22.0056-5.0873-8.77042.01864.9937.4697-0.01320.7905-1.5747-0.557-0.2962-0.04550.1396-0.9240.31260.7194-0.01470.160.9129-0.22430.9626-17.02253.54422.4197
38.15540.2155-1.26662.00541.99712.00080.1579-0.1006-0.5587-0.0891-0.1714-0.37071.30070.98290.04110.46940.0781-0.08210.2403-0.05950.5331-8.20734.7517-44.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 254
2X-RAY DIFFRACTION2chain B and resid 302:317B302 - 317
3X-RAY DIFFRACTION3chain B and resid 328:354B328 - 354

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