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- PDB-5y04: Crystal Structure of the complex between the vinculin D1 domain a... -

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Basic information

Entry
Database: PDB / ID: 5y04
TitleCrystal Structure of the complex between the vinculin D1 domain and alphaE-catenin
Components
  • Catenin alpha-1
  • Vinculin
KeywordsCELL ADHESION / ADHERENS JUNCTION / CYTOSKELETON
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / VEGFR2 mediated vascular permeability / terminal web / Adherens junctions interactions / MAP2K and MAPK activation / RHO GTPases activate IQGAPs ...negative regulation of integrin-mediated signaling pathway / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / VEGFR2 mediated vascular permeability / terminal web / Adherens junctions interactions / MAP2K and MAPK activation / RHO GTPases activate IQGAPs / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / Smooth Muscle Contraction / fascia adherens / cellular response to indole-3-methanol / Platelet degranulation / dystroglycan binding / alpha-catenin binding / flotillin complex / vinculin binding / cell-cell contact zone / Myogenesis / catenin complex / apical junction assembly / costamere / regulation of establishment of endothelial barrier / negative regulation of cell motility / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / axon extension / adherens junction assembly / negative regulation of protein localization to nucleus / protein localization to cell surface / podosome / axon regeneration / lamellipodium assembly / regulation of focal adhesion assembly / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / brush border / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / Neutrophil degranulation / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / regulation of cell migration / morphogenesis of an epithelium / integrin-mediated signaling pathway / cell projection / adherens junction / cell motility / sarcolemma / beta-catenin binding / small GTPase binding / response to estrogen / male gonad development / Z disc / actin filament binding / cell-cell junction / intracellular protein localization / lamellipodium / actin cytoskeleton / regulation of cell population proliferation / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / structural molecule activity / Golgi apparatus / protein-containing complex / identical protein binding / nucleus / 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
Catenin alpha-1 / Vinculin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsHirano, Y. / Hakoshima, T.
CitationJournal: Genes Cells / Year: 2018
Title: The force-sensing device region of alpha-catenin is an intrinsically disordered segment in the absence of intramolecular stabilization of the autoinhibitory form
Authors: Hirano, Y. / Amano, Y. / Yonemura, S. / Hakoshima, T.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Vinculin
B: Catenin alpha-1


Theoretical massNumber of molelcules
Total (without water)39,5112
Polymers39,5112
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-39 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.807, 73.825, 111.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vinculin / Metavinculin


Mass: 28100.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vcl / Plasmid: PET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q64727
#2: Protein Catenin alpha-1 / 102 kDa cadherin-associated protein / Alpha E-catenin / CAP102


Mass: 11410.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 276-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna1, Catna1 / Plasmid: PET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: P26231
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 100MM IMIDAZOLE, 0.5-0.7M POTASSIUM TARTRATE, 0.35M SODIUM FORMATE
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9785, 0.9788, 0.9946
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 19, 2009 / Details: MIRRORS
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR , SI (111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97881
30.99461
ReflectionResolution: 2.85→50 Å / Num. obs: 10287 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.052 / Net I/σ(I): 41.4
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.425 / % possible all: 73.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MAD / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 34.624 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.053 / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.281 501 4.8 %RANDOM
Rwork0.247 ---
obs0.248 10000 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94 Å2
Baniso -1Baniso -2Baniso -3
1-4.28 Å2-0 Å20 Å2
2--1.03 Å2-0 Å2
3----5.31 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 0 6 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9853043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6755297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.86225.06281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82815390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6731513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 19 -
Rwork0.336 443 -
obs--61.35 %
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)
10.37520.5753-0.82371.4917-1.68342.8440.1198-0.02180.13380.16190.00510.0874-0.0716-0.0066-0.12490.1808-0.03620.0140.2318-0.00650.10910.64819.742317.1073
20.45270.0254-0.07710.7985-0.03250.01590.13290.19650.40510.1201-0.06830.1648-0.0202-0.0556-0.06450.3303-0.08380.11270.46690.08960.41113.280127.48089.2323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B306 - 373

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