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- PDB-1rkc: Human vinculin head (1-258) in complex with talin's vinculin bind... -

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Basic information

Entry
Database: PDB / ID: 1rkc
TitleHuman vinculin head (1-258) in complex with talin's vinculin binding site 3 (residues 1944-1969)
Components
  • Talin
  • Vinculin
Keywordscell adhesion / structural protein / cytoskeleton / actin-binding / x-ray crystallography
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / ruffle / negative regulation of cell migration / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / sarcolemma / beta-catenin binding / platelet aggregation / ruffle membrane / cell-cell adhesion / 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 / cell-cell junction / extracellular vesicle / actin filament binding / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / actin binding / secretory granule lumen / 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 / cell surface / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vinculin repeated domain signature. / : / Talin, R4 domain / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment ...Vinculin repeated domain signature. / : / Talin, R4 domain / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsIzard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
CitationJournal: Nature / Year: 2004
Title: Vinculin activation by talin through helical bundle conversion
Authors: Izard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Talin


Theoretical massNumber of molelcules
Total (without water)32,3952
Polymers32,3952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-22 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.680, 155.680, 155.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Vinculin


Mass: 29489.982 Da / Num. of mol.: 1 / Fragment: vinculin head (residues 1-258)
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
#2: Protein/peptide Talin


Mass: 2905.392 Da / Num. of mol.: 1 / Fragment: binding site 3 (residues 1944-1969)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P54939

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / pH: 4
Details: 2% MPD; 100 mM citric acid (pH 4); 100 mM CdCl2, pH 4.0, temperature 293K
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %MPD1reservoir
2100 mMcitric acid1reservoirpH4
3100 mM1reservoirCdCl

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,1.2545,0.9793
DetectorDetector: CCD
RadiationProtocol: MIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.25451
ReflectionResolution: 2.7→15 Å / Num. all: 9051 / Num. obs: 9051 / Observed criterion σ(I): 0 / Biso Wilson estimate: 99.3 Å2
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 45 Å / Num. all: 9121 / % possible obs: 99.8 % / Redundancy: 19.6 % / Num. measured all: 178681 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / % possible obs: 99.7 % / Redundancy: 5.4 % / Num. unique obs: 1290 / Num. measured obs: 6993 / Rmerge(I) obs: 0.497

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALAdata scaling
SHARPphasing
BUSTER-TNTrefinement
d*TREKdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.335 433 4.8 %RANDOM
Rwork0.244 ---
all-9051 --
obs-9051 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 90 Å2
Displacement parametersBiso mean: 111.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 0 0 2223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.263
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
LS refinement shellResolution: 2.7→2.78 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.248 / Total num. of bins used: 9
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_bond_d / Dev ideal: 0.01
LS refinement shell
*PLUS
Highest resolution: 2.7 Å

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