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- PDB-3zdl: Vinculin head (1-258) in complex with a RIAM fragment -

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Basic information

Entry
Database: PDB / ID: 3zdl
TitleVinculin head (1-258) in complex with a RIAM fragment
Components
  • AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN
  • VINCULIN
KeywordsCELL ADHESION
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / terminal web / epithelial cell-cell adhesion ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / T cell receptor complex / regulation of focal adhesion assembly / p130Cas linkage to MAPK signaling for integrins / alpha-actinin binding / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / skeletal muscle myofibril / positive regulation of cell adhesion / stress fiber / regulation of cell migration / Integrin signaling / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / neuromuscular junction / MAP2K and MAPK activation / Z disc / beta-catenin binding / 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 / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / lamellipodium / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / signal transduction / protein homodimerization activity / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Ras association (RalGDS/AF-6) domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family ...GRB/APBB1IP / APBB1IP, PH domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Ras association (RalGDS/AF-6) domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Alpha-catenin/vinculin-like superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vinculin / Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZacharchenko, T. / Elliott, P.R. / Goult, B.T. / Bate, N. / Critchely, D.R. / Barsukov, I.L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Riam and Vinculin Binding to Talin are Mutually Exclusive and Regulate Adhesion Assembly and Turnover.
Authors: Goult, B.T. / Zacharchenko, T. / Bate, N. / Tsang, R. / Hey, F. / Gingras, A.R. / Elliott, P.R. / Roberts, G.C. / Ballestrem, C. / Critchley, D.R. / Barsukov, I.L.
History
DepositionNov 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Derived calculations / Other
Revision 1.3Apr 10, 2013Group: Derived calculations / Other
Revision 1.4Apr 17, 2013Group: Database references
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VINCULIN
B: AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,8672
Polymers34,8672
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-27.8 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.730, 70.030, 95.600
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: 31327.104 Da / Num. of mol.: 1 / Fragment: VD1 DOMAIN, RESIDUES 1-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN / APBB1-INTERACTING PROTEIN 1 / PROLINE-RICH EVH1 LIGAND 1 / PREL-1 / PROLINE-RICH PROTEIN 73 / RAP1- ...APBB1-INTERACTING PROTEIN 1 / PROLINE-RICH EVH1 LIGAND 1 / PREL-1 / PROLINE-RICH PROTEIN 73 / RAP1-GTP-INTERACTING ADAPTER MOLECULE / RIAM / RETINOIC ACID-RESPONSIVE PROLINE-RICH PROTEIN 1 / RARP-1


Mass: 3539.914 Da / Num. of mol.: 1 / Fragment: N TERMINAL DOMAIN, RESIUDES 1-32 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7Z5R6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC TERMINAL TYROSINE NON NATIVE

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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: 2.79 Å3/Da / Density % sol: 55.96 % / Description: NONE
Crystal growDetails: 1.2M AMMONIUM SULPHATE, 0.05M TRI-SODIUM CITRATE, 3% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2011
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→56.49 Å / Num. obs: 16055 / % possible obs: 100 % / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWJ

1xwj


Resolution: 2.3→47.8 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 801 5 %
Rwork0.1881 --
obs0.1901 16016 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 57 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082230
X-RAY DIFFRACTIONf_angle_d1.093018
X-RAY DIFFRACTIONf_dihedral_angle_d15.857852
X-RAY DIFFRACTIONf_chiral_restr0.064371
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.3491090.24232491X-RAY DIFFRACTION100
2.4441-2.63280.25821440.20942487X-RAY DIFFRACTION100
2.6328-2.89770.24921480.19912494X-RAY DIFFRACTION100
2.8977-3.3170.26371360.18312516X-RAY DIFFRACTION100
3.317-4.17860.18951300.16762552X-RAY DIFFRACTION100
4.1786-47.81040.2081340.18442675X-RAY DIFFRACTION100
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)
10.7701-0.53351.16640.644-0.68361.08890.08980.1576-0.0243-0.1971-0.0721-0.03550.05060.07420.01120.11890.02120.01760.14730.03810.1037-11.0375-13.693823.4492
21.01560.3822-0.41052.2228-0.86013.57010.0662-0.0446-0.08380.04240.22030.07950.2479-0.40660.08890.3363-0.0166-0.16590.20540.02750.7093-11.5667-27.7443.7533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:256)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 7:32)

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