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- PDB-2h7d: Solution structure of the talin F3 domain in complex with a chime... -

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Basic information

Entry
Database: PDB / ID: 2h7d
TitleSolution structure of the talin F3 domain in complex with a chimeric beta3 integrin-PIP kinase peptide
Components
  • Chimera of 24-mer peptide from Integrin beta-3 and 10-mer peptide from Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
  • Talin-1
KeywordsSTRUCTURAL PROTEIN / Protein-peptide complex / alpha helix / beta sheet
Function / homology
Function and homology information


talin binding / 1-phosphatidylinositol-4-phosphate 5-kinase / 1-phosphatidylinositol-4-phosphate 5-kinase activity / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Synthesis of PIPs at the plasma membrane / uropod / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex ...talin binding / 1-phosphatidylinositol-4-phosphate 5-kinase / 1-phosphatidylinositol-4-phosphate 5-kinase activity / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Synthesis of PIPs at the plasma membrane / uropod / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of postsynaptic neurotransmitter receptor diffusion trapping / phosphatidylinositol metabolic process / Clathrin-mediated endocytosis / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / phosphatidylinositol biosynthetic process / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / exocytosis / PECAM1 interactions / regulation of synaptic vesicle endocytosis / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / phagocytic cup / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / phagocytosis / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / ruffle / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / axonogenesis / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway
Similarity search - Function
Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily ...Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 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, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / 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, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / FERM domain signature 2. / Integrin domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma / Integrin beta-3 / Talin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsWegener, K.L.
CitationJournal: CELL(CAMBRIDGE,MASS.) / Year: 2007
Title: Structural basis of integrin activation by talin
Authors: Wegener, K.L. / Partridge, A.W. / Han, J. / Pickford, A.R. / Liddington, R.C. / Ginsberg, M.H. / Campbell, I.D.
History
DepositionJun 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Chimera of 24-mer peptide from Integrin beta-3 and 10-mer peptide from Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma


Theoretical massNumber of molelcules
Total (without water)15,7552
Polymers15,7552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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: 11475.312 Da / Num. of mol.: 1 / Fragment: F3 domain / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TLN1, TLN / Plasmid: pGEX-6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54939
#2: Protein/peptide Chimera of 24-mer peptide from Integrin beta-3 and 10-mer peptide from Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma / Chimera of beta3-integrin and PIP-kinase


Mass: 4279.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P05106, UniProt: O70161
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1332D NOESY
1442D NOESY
151HMQCJ
1652D 1H-15N-13C

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM Talin F3 U-15N; 1.4mM chimeric peptide; 50mM phosphate buffer pH 6.1, 100mM NaCl; 95% H2O, 5% D2O95% H2O/5% D2O
21.5mM Talin F3; 1.5mM chimeric peptide; 50mM phosphate buffer pH 6.1, 100mM NaCl; 99.96% D2O99.96% D2O
31.9mM Talin F3 U-15N,2H; 1.5mM chimeric peptide; 50mM phosphate buffer pH 6.1, 100mM NaCl; 95% H2O, 5% D2O95% H2O/5% D2O
41.9mM Talin F3 U-15N,2H; 1.5mM chimeric peptide; 50mM phosphate buffer pH 6.1, 100mM NaCl; 99.96% D2O99.96% D2O
50.9mM Talin F3 U-15N,13C; 1.1mM chimeric peptide; 50mM phosphate buffer pH 6.1, 100mM NaCl; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built home builtHome-builthome built5001
Home-built home builtHome-builthome built6002
Home-built home builtHome-builthome built7503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
NMRPipe2004Delaglioprocessing
Sparky3.11Goddard and Knellerdata analysis
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2175 restraints, of which 2015 are NOE-derived distance restraints, 126 dihedral angle restraints and 34 distance restraints from hydrogen bonds.
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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