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- PDB-2l10: Solution Structure of the R6 Domain of Talin -

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Basic information

Entry
Database: PDB / ID: 2l10
TitleSolution Structure of the R6 Domain of Talin
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / Talin / Helical Bundle / Cytoskeleton / Focal Adhesion
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
Talin, central domain / A middle domain of Talin 1 / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site ...Talin, central domain / A middle domain of Talin 1 / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsGoult, B.T. / Gingras, A.R. / Bate, N. / Roberts, G.C.K. / Barsukov, I.L. / Critchley, D.R.
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
DepositionJul 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Aug 25, 2021Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)16,4881
Polymers16,4881
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Talin-1


Mass: 16488.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / 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
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D 1H-13C NOESY
1413D 1H-15N TOCSY
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNCA
1823D HNCO
1923D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] C-1, 5 % [U-100% 2H] D2O-2, 2 mM DTT-3, 50 mM sodium chloride-4, 20 mM TRIS-5, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] C-6, 5 % [U-100% 2H] D2O-7, 2 mM DTT-8, 50 mM sodium chloride-9, 20 mM TRIS-10, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-1[U-100% 15N]1
5 %D2O-2[U-100% 2H]1
2 mMDTT-31
50 mMsodium chloride-41
20 mMTRIS-51
1 mMC-6[U-100% 13C; U-100% 15N]2
5 %D2O-7[U-100% 2H]2
2 mMDTT-82
50 mMsodium chloride-92
20 mMTRIS-102
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CCPNmr1.13CCPNchemical shift assignment
CCPNmr1.13CCPNrefinement
CCPNmr1.13CCPNdata analysis
CCPNmr1.13CCPNpeak picking
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesgeometry optimization
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Final Structures refined in explicit water bath as implemented in Aria1.2/CNS1.2. 20 lowest energy structures selected from water refinement, initial structures generated with cyana
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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