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- PDB-2l7n: Solution Structure of the R5 Domain of Talin -

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Basic information

Entry
Database: PDB / ID: 2l7n
TitleSolution Structure of the R5 Domain of Talin
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / Integrin / Bundle / Focal Adhesion
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 / platelet aggregation / ruffle membrane / cell-cell adhesion / 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 / : / Talin, R4 domain / 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, central domain / A middle domain of Talin 1 / : / Talin, R4 domain / 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 / 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. / Barsukov, I.L. / Roberts, G.C.K. / 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
DepositionDec 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Aug 25, 2021Group: Data collection / Database references / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / struct / 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.title / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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)17,3511
Polymers17,3511
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: 17350.570 Da / Num. of mol.: 1 / Fragment: sequence database residues 1046-1207
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
1313D 1H-15N NOESY
1423D 1H-13C NOESY
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D (H)CCH-TOCSY
1923D HN(CO)CA
11023D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] DomB, 10 % [U-100% 2H] D2O, 90 % H2O, 2 mM DTT, 50 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] DomB, 10 % [U-100% 2H] D2O, 90 % H2O, 2 mM DTT, 50 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDomB-1[U-100% 15N]1
10 %D2O-2[U-100% 2H]1
90 %H2O-31
2 mMDTT-41
50 mMsodium chloride-51
20 mMsodium phosphate-61
1 mMDomB-7[U-100% 13C; U-100% 15N]2
10 %D2O-8[U-100% 2H]2
90 %H2O-92
2 mMDTT-102
50 mMsodium chloride-112
20 mMsodium phosphate-122
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 DRXBrukerDRX6001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
ARIA1.2Linge, O'Donoghue and Nilgesgeometry optimization
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: FINAL STRUCTURES REFINED IN EXPLICIT WATER BATH AS IMPLEMENTED IN ARIA 1.2/CNS 1.1. 20 LOWEST ENERGY STRUCTURES SELECTED FROM WATER REFINEMENT, CNS, INITIAL STRUCTURES GENERATED WITH CYANA
NMR constraintsNOE constraints total: 3405 / NOE intraresidue total count: 1474 / NOE long range total count: 487 / NOE medium range total count: 584 / NOE sequential total count: 860
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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