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- PDB-2b0h: Solution structure of VBS3 fragment of talin -

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Basic information

Entry
Database: PDB / ID: 2b0h
TitleSolution structure of VBS3 fragment of talin
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / talin / vinculin / helical bundle / VBS
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Platelet degranulation / vinculin binding / integrin activation ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Platelet degranulation / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / phosphatidylserine binding / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / ruffle membrane / platelet aggregation / cell-cell adhesion / actin filament binding / integrin binding / cytoskeleton / focal adhesion / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / Talin, R4 domain / 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 ...: / Talin, R4 domain / 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 / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics torsion angle dynamics
AuthorsGingras, A.R. / Vogel, K.P. / Steinhoff, H.J. / Ziegler, W.H. / Patel, B. / Emsley, J. / Critchley, D.R. / Roberts, G.C. / Barsukov, I.L.
CitationJournal: Biochemistry / Year: 2006
Title: Structural and Dynamic Characterization of a Vinculin Binding Site in the Talin Rod
Authors: Gingras, A.R. / Vogel, K.P. / Steinhoff, H.J. / Ziegler, W.H. / Patel, B. / Emsley, J. / Critchley, D.R. / Roberts, G.C. / Barsukov, I.L.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Talin-1


Theoretical massNumber of molelcules
Total (without water)14,5841
Polymers14,5841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
Representative

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Components

#1: Protein Talin-1


Mass: 14584.450 Da / Num. of mol.: 1 / Fragment: residues 1843-1973
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pET-151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P26039

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 15N-separated NOESY
1223D 13C-separated NOESY
1313D 13C-separated NOESY
1442D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM talin 1843-1973 [15N,13C]; 20 mM phosphate, (pH 6.5), 50 mM NaCl, 2 mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
21.5 mM talin 1843-1973 [15N,13C]; 20 mM phosphate, (pH 6.5), 50 mM NaCl, 2 mM DTT, 100% D2O100% D2O
31.0 mM talin 1843-1973 [15N]; 20 mM phosphate, (pH 6.5), 50 mM NaCl, 2 mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
41.0 mM talin 1843-1973; 20 mM phosphate, (pH 6.5), 50 mM NaCl, 2 mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Peter Guntertstructure solution
NMRPipe2005Frank Delaglioprocessing
CNS1.1A.T. Brungerrefinement
ARIA1.2M. Nilgesstructure solution
XwinNMR3.6Brukercollection
NMRView5.0.16B.A. Johnsondata analysis
RefinementMethod: distance geometry simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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