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- PDB-2kma: NMR structure of the F0F1 double domain (residues 1-202) of the t... -

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Basic information

Entry
Database: PDB / ID: 2kma
TitleNMR structure of the F0F1 double domain (residues 1-202) of the talin ferm domain
ComponentsTalin 1
KeywordsSTRUCTURAL PROTEIN / TALIN / FERM / F0 / N-TERMINAL / F1 / ADHESION / CYTOPLASM / CYTOSKELETON / MEMBRANE
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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS, TORSION ANGLE DYNAMICS
Model detailslowest energy
AuthorsGoult, B.T. / Elliott, P.R. / Bate, N. / Roberts, G.C. / 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
DepositionJul 25, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 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: Talin 1


Theoretical massNumber of molelcules
Total (without water)20,6861
Polymers20,6861
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: 20685.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-138, RESIDUES 169-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RP23-195K8.11-001, TLN, Tln1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2AIM8, UniProt: P26039*PLUS
Sequence detailsFUSION PROTEIN OF RESIDUES 1-138 AND RESIDUES 169-202

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D (H)CCH-TOCSY
1323D CBCA(CO)NH
1423D HN(CA)CB
1513D 1H-15N NOESY
1623D 1H-13C NOESY
1723D HBHA(CO)NH
1823D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] F0F1-1, 50 mM sodium chloride-2, 2 mM DTT-3, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] F0F1-4, 50 mM sodium chloride-5, 2 mM DTT-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMF0F1-1[U-100% 15N]1
50 mMsodium chloride-21
2 mMDTT-31
0.8 mMF0F1-4[U-100% 13C; U-100% 15N]2
50 mMsodium chloride-52
2 mMDTT-62
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
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CcpNmr Analysis1.15CCPNchemical shift assignment
CcpNmr Analysis1.15CCPNdata analysis
CcpNmr Analysis1.15CCPNpeak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichgeometry optimization
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
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: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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