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- PDB-9qwo: Vinculin tail bound to paxillin LD2 -

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Basic information

Entry
Database: PDB / ID: 9qwo
TitleVinculin tail bound to paxillin LD2
Components
  • Isoform 1 of Vinculin
  • Isoform Gamma of Paxillin
  • Paxillin
KeywordsCELL ADHESION / Focal Adhesions / Force Transduction / Vinculin / Paxillin
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / 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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / 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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / neuropilin binding / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / signal complex assembly / axon extension / protein localization to cell surface / microtubule associated complex / lamellipodium assembly / growth hormone receptor signaling pathway / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / GAB1 signalosome / endothelial cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / 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 / cellular response to reactive oxygen species / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / VEGFA-VEGFR2 Pathway / 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 / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / cell-cell junction / Platelet degranulation / cell migration / extracellular vesicle / lamellipodium / actin binding / cell cortex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphatase binding / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / signal transduction / protein-containing complex / extracellular exosome / extracellular region / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Paxillin / : / : / Paxillin family / Vinculin repeated domain signature. / Vinculin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family ...Paxillin / : / : / Paxillin family / Vinculin repeated domain signature. / Vinculin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile.
Similarity search - Domain/homology
ACETATE ION / Paxillin / Vinculin / Paxillin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsDiaz-Palacios, K. / Lietha, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentPID2021-127058NB-I00 Spain
CitationJournal: Cell Commun Signal / Year: 2025
Title: Phospho-regulated tethering of focal adhesion kinase to vinculin links force transduction to focal adhesion signaling.
Authors: Diaz-Palacios, K. / Lopez Navajas, P. / Rodrigo Martin, B. / Matesanz, R. / Luque-Ortega, J.R. / Echarri, A. / Lietha, D.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1 of Vinculin
B: Isoform 1 of Vinculin
E: Isoform Gamma of Paxillin
G: Paxillin
C: Isoform 1 of Vinculin
D: Isoform 1 of Vinculin
F: Isoform Gamma of Paxillin
H: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,24726
Polymers87,8888
Non-polymers1,35918
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Analytical Ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-155 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.382, 70.562, 117.372
Angle α, β, γ (deg.)90.00, 131.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isoform 1 of Vinculin / Metavinculin / MV


Mass: 20171.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / References: UniProt: P18206

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Protein/peptide , 2 types, 4 molecules EFGH

#2: Protein/peptide Isoform Gamma of Paxillin


Mass: 2180.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49023
#3: Protein/peptide Paxillin


Mass: 1420.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A1B0GTU4

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Non-polymers , 3 types, 117 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 1.26 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na Acetate pH4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 2.54→44.87 Å / Num. obs: 35621 / % possible obs: 99.6 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.069 / Rrim(I) all: 0.124 / Net I/σ(I): 7.3
Reflection shellResolution: 2.55→2.69 Å / % possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.856 / Num. measured all: 16149 / Num. unique obs: 5168 / CC1/2: 0.611 / Rpim(I) all: 0.575 / Rrim(I) all: 1.035 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→44.87 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.451 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25909 1677 4.7 %RANDOM
Rwork0.22522 ---
obs0.22675 34219 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.2 Å2
2---0.14 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.54→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 80 99 5922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165911
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.8447826
X-RAY DIFFRACTIONr_angle_other_deg0.3691.79813556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6755730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.812560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.444101191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021257
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_it0.5470.5812960
X-RAY DIFFRACTIONr_mcbond_other0.5020.5642950
X-RAY DIFFRACTIONr_mcangle_it0.8781.0023670
X-RAY DIFFRACTIONr_mcangle_other0.8791.0033671
X-RAY DIFFRACTIONr_scbond_it0.8490.6922880
X-RAY DIFFRACTIONr_scbond_other0.8490.6942881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1521.2854157
X-RAY DIFFRACTIONr_long_range_B_refined6.0775.226535
X-RAY DIFFRACTIONr_long_range_B_other6.0765.236536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.543→2.608 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 109 -
Rwork0.141 2321 -
obs--90.57 %
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)
13.7781-1.11952.39042.8537-0.85652.61650.03650.1841-0.32880.03940.03960.24560.1057-0.0453-0.0760.5528-0.0404-0.46340.3088-0.02681.0743-30.902-10.66910.609
23.5752-0.6495-0.33385.2962-2.16186.37670.27820.25440.1162-0.3524-0.268-0.24820.18150.839-0.01030.55350.0368-0.4750.4683-0.07240.97024.053-13.40226.382
325.2795-15.3504-10.653910.78796.734822.61810.58981.0422-1.0681-0.5197-0.62810.6534-1.276-0.86770.03820.2811-0.014-0.35490.08890.09260.7074-16.667-18.19425.576
426.1924-6.15299.49277.128-1.837222.63630.4696-0.14260.7335-0.7127-0.3720.23790.2148-0.0825-0.09760.1753-0.0167-0.2340.06310.05680.7697-22.114-25.98925.039
52.8541-0.81572.22742.6284-0.83463.8043-0.1029-0.01670.14460.2916-0.017-0.0316-0.31640.1820.11980.6435-0.0338-0.47380.3023-0.02571.0287-6.55412.1132.071
65.4258-2.3398-0.38165.5611-0.27233.6448-0.02530.85350.0946-0.2255-0.2467-0.26240.1620.2010.27210.5287-0.0557-0.47810.43540.02220.9977-26.60614.839-0.618
719.35383.2264-10.06999.8474-15.25325.61520.0129-0.9142-1.11420.4538-0.7655-0.401-0.68981.36130.75270.39060.0617-0.37610.1147-0.03360.4895-23.1919.6419.832
821.79831.55895.326310.5524-3.559219.6444-0.3059-0.2020.2960.6229-0.2693-0.7560.5562-0.2320.57510.46960.0533-0.32410.0402-0.03760.3237-21.96527.43725.164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A892 - 1066
2X-RAY DIFFRACTION2B887 - 1060
3X-RAY DIFFRACTION3C309 - 324
4X-RAY DIFFRACTION4D324 - 336
5X-RAY DIFFRACTION5E892 - 1066
6X-RAY DIFFRACTION6F887 - 1060
7X-RAY DIFFRACTION7G309 - 324
8X-RAY DIFFRACTION8H324 - 336

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