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- PDB-2kc1: NMR structure of the F0 domain (residues 0-85) of the talin ferm ... -

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Basic information

Entry
Database: PDB / ID: 2kc1
TitleNMR structure of the F0 domain (residues 0-85) of the talin ferm domain
ComponentsMKIAA1027 protein
KeywordsSTRUCTURAL PROTEIN / TALIN / FERM / F0 / integrin / CYTOSKELETON / Rap1
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, 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 ...: / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Talin-1 / MKIAA1027 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS, TORSION ANGLE DYNAMICS
AuthorsGoult, B.T. / Elliott, P.R. / Roberts, G.C.K. / Critchley, D.R. / Barsukov, I.L.
CitationJournal: Embo J. / Year: 2010
Title: Structure of a double ubiquitin-like domain in the talin head: a role in integrin activation.
Authors: Goult, B.T. / Bouaouina, M. / Elliott, P.R. / Bate, N. / Patel, B. / Gingras, A.R. / Grossmann, J.G. / Roberts, G.C. / Calderwood, D.A. / Critchley, D.R. / Barsukov, I.L.
History
DepositionDec 13, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: MKIAA1027 protein


Theoretical massNumber of molelcules
Total (without water)10,3331
Polymers10,3331
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 MKIAA1027 protein / F0 / Talin-1


Mass: 10332.973 Da / Num. of mol.: 1 / Fragment: N-TERMINAL RESIDUES 0-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mKIAA1027, TLN, Tln1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q80TM2, UniProt: P26039*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1923D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] F0-1, 10 % [U-100% 2H] D2O-2, 2 mM DTT-3, 50 mM sodium chloride-4, 20 mM sodium phosphate-5, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] F0-6, 10 % [U-100% 2H] D2O-7, 2 mM DTT-8, 50 mM sodium chloride-9, 20 mM sodium phosphate-10, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMF0-1[U-100% 13C; U-100% 15N]1
10 %D2O-2[U-100% 2H]1
2 mMDTT-31
50 mMsodium chloride-41
20 mMsodium phosphate-51
1 mMF0-6[U-100% 15N]2
10 %D2O-7[U-100% 2H]2
2 mMDTT-82
50 mMsodium chloride-92
20 mMsodium phosphate-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 DRXBrukerDRX6001
BRUKER DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2LINGE, O'DONOGHUErefinement
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CCPNMR1.15CCPNchemical shift assignment
CCPNMR1.15CCPNpeak picking
CCPNMR1.15CCPNdata analysis
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
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 / Representative conformer: 1

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