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- PDB-5l0g: Human metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1... -

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Basic information

Entry
Database: PDB / ID: 5l0g
TitleHuman metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2
ComponentsVinculin
KeywordsCELL ADHESION / 5-Helix bundle / cytoskelatal protein / phospholipids / structural protein
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding / alpha-catenin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / adherens junction assembly / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / morphogenesis of an epithelium / cell projection / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / beta-catenin binding / sarcolemma / platelet aggregation / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / Platelet degranulation / extracellular vesicle / actin binding / secretory granule lumen / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChinthalapudi, K. / Izard, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Differential lipid binding of vinculin isoforms promotes quasi-equivalent dimerization.
Authors: Chinthalapudi, K. / Rangarajan, E.S. / Brown, D.T. / Izard, T.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: Vinculin
C: Vinculin
D: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1446
Polymers78,6514
Non-polymers1,4932
Water82946
1
B: Vinculin
hetero molecules

A: Vinculin


Theoretical massNumber of molelcules
Total (without water)40,0723
Polymers39,3252
Non-polymers7471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z+1/31
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area18740 Å2
MethodPISA
2
C: Vinculin
hetero molecules

D: Vinculin


Theoretical massNumber of molelcules
Total (without water)40,0723
Polymers39,3252
Non-polymers7471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z+1/31
Buried area1360 Å2
ΔGint-12 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.858, 56.858, 193.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsDimer confirmed by In vitro FRET analysis

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Components

#1: Protein
Vinculin / Metavinculin / MV


Mass: 19662.748 Da / Num. of mol.: 4 / Fragment: UNP Residues 959-1134 / Mutation: Q971R, R975D, T978R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18206
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 12% PEG 3350, 2% tryptone, and 0.05 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 9, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→96.57 Å / Num. obs: 9632 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 86.68 Å2 / CC1/2: 0.983 / Rpim(I) all: 0.103 / Net I/σ(I): 8.5
Reflection shellResolution: 3.4→3.73 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 3.6 / CC1/2: 0.906 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MYI

3myi


Resolution: 3.4→49.24 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.8902 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.598
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 473 4.94 %RANDOM
Rwork0.1797 ---
obs0.1841 9571 99.72 %-
Displacement parametersBiso mean: 96.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.1743 Å20 Å20 Å2
2--3.1743 Å20 Å2
3----6.3486 Å2
Refine analyzeLuzzati coordinate error obs: 0.744 Å
Refinement stepCycle: LAST / Resolution: 3.4→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 56 46 5424
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015416HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.147304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2735SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes762HARMONIC5
X-RAY DIFFRACTIONt_it5416HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion783SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6399SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.8 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.275 138 5.05 %
Rwork0.1973 2593 -
all0.201 2731 -
obs--99.72 %

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