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- PDB-2kbb: Solution Structure of the R9 Domain of Talin -

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Basic information

Entry
Database: PDB / ID: 2kbb
TitleSolution Structure of the R9 Domain of Talin
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / TALIN / ROD / BUNDLE / integrin / F3 / CYTOSKELETON / AUTOINHIBITION / Cell membrane / Cell projection / Cytoplasm / Membrane / Phosphoprotein
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, 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
AuthorsGoult, B.T. / Gingras, A.R. / Bate, N. / Critchley, D.R. / Barsukov, I.L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The structure of an interdomain complex that regulates talin activity.
Authors: Goult, B.T. / Bate, N. / Anthis, N.J. / Wegener, K.L. / Gingras, A.R. / Patel, B. / Barsukov, I.L. / Campbell, I.D. / Roberts, G.C. / Critchley, D.R.
History
DepositionNov 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 25, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / 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 1.3May 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)18,2471
Polymers18,2471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8100 Å2
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


Mass: 18247.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 1655-1822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln, Tln1 / Plasmid: PET-151 / 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 CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D HN(CO)CA
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] TALIN-1, 10 % [U-100% 2H] D2O, 50 mM sodium chloride, 2 mM DTT, 50 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] TALIN-1, 10 % [U-100% 2H] D2O, 50 mM sodium chloride, 2 mM DTT, 50 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTALIN-1[U-100% 15N]1
10 %D2O[U-100% 2H]1
50 mMsodium chloride1
2 mMDTT1
50 mMsodium phosphate1
1 mMTALIN-1[U-100% 13C; U-100% 15N]2
10 %D2O[U-100% 2H]2
50 mMsodium chloride2
2 mMDTT2
50 mMsodium phosphate2
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER DRXBrukerDRX6001
BRUKER DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, J.P. et al.refinement
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CcpNmr Analysis1.015CCPNchemical shift assignment
CcpNmr Analysis1.015CCPNpeak picking
CcpNmr Analysis1.015CCPNdata analysis
CYANA2.1Guntert, P. et al.structure solution
CYANA2.1Guntert, P. et al.peak picking
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 USING CNS. INITIAL STRUCTURES GENERATED WITH CYANA.
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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