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- PDB-1u89: Solution structure of VBS2 fragment of talin -

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Basic information

Entry
Database: PDB / ID: 1u89
TitleSolution structure of VBS2 fragment of talin
ComponentsTalin 1
KeywordsSTRUCTURAL PROTEIN / 4-helix bundle / left-handed
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Smooth Muscle Contraction / MAP2K and MAPK activation / Platelet degranulation / LIM domain binding / cortical microtubule organization / vinculin binding ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Smooth Muscle Contraction / MAP2K and MAPK activation / Platelet degranulation / LIM domain binding / cortical microtubule organization / 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 / cell-cell adhesion / ruffle membrane / actin filament binding / integrin binding / cytoskeleton / focal adhesion / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site / Talin, middle domain ...Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin IBS2B domain / Talin, N-terminal F0 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 / IRS-type PTB domain / PTB domain (IRS-1 type) / 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, tortion angle dynamics, simmulated annealing
AuthorsFillingham, I. / Gingras, A.R. / Papagrigoriou, E. / Patel, B. / Emsley, J. / Roberts, G.C.K. / Critchley, D.R. / Barsukov, I.L.
CitationJournal: Structure / Year: 2005
Title: A vinculin binding domain from the talin rod unfolds to form a complex with the vinculin head.
Authors: Fillingham, I. / Gingras, A.R. / Papagrigoriou, E. / Patel, B. / Emsley, J. / Critchley, D.R. / Roberts, G.C. / Barsukov, I.L.
History
DepositionAug 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 29, 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)14,3971
Polymers14,3971
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
RepresentativeModel #1lowest energy

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Components

#1: Protein Talin 1 / talin


Mass: 14396.910 Da / Num. of mol.: 1 / Fragment: vbs2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26039

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 13C-separated NOESY
1333D 15N-separated NOESY
1442D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM talin 755-889 U-15N, 13C; 20mM phosphate buffer, 20mM NaCl, 0.02% NaN390% H2O/10% D2O
21.5mM talin 755-889 U-15N, 13C; 20mM phosphate buffer, 20mM NaCl, 0.02% NaN3100% D2O
31.5mM talin 755-889 U-15N; 20mM phosphate buffer, 20mM NaCl, 0.02% NaN390% H2O/10% D2O
41.5mM talin 755-889; 20mM phosphate buffer, 20mM NaCl, 0.02% NaN3100% D2O
Sample conditionsIonic strength: 20mM phosphate, 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 303 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 DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2003Delaglio, F.processing
NMRView5.0.16Johnson, B.A.data analysis
CYANA1.0.6Guntert, P.structure solution
ARIA1.2Nilges, M.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: distance geometry, tortion angle dynamics, simmulated annealing
Software ordinal: 1
Details: The structure is based on 3018 NOE distance restraints and 176 dihedral talos restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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