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- PDB-1y19: Structural basis for phosphatidylinositol phosphate kinase type I... -

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Basic information

Entry
Database: PDB / ID: 1y19
TitleStructural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions
Components
  • Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
  • Talin 1
KeywordsSTRUCTURAL PROTEIN / SIGNALING PROTEIN / FOCAL ADHESION / FERM DOMAIN / CYTOSKELETON / NPXY MOTIF / PTB DOMAIN
Function / homology
Function and homology information


talin binding / 1-phosphatidylinositol-4-phosphate 5-kinase / 1-phosphatidylinositol-4-phosphate 5-kinase activity / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Synthesis of PIPs at the plasma membrane / uropod ...talin binding / 1-phosphatidylinositol-4-phosphate 5-kinase / 1-phosphatidylinositol-4-phosphate 5-kinase activity / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Synthesis of PIPs at the plasma membrane / uropod / LIM domain binding / Smooth Muscle Contraction / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phosphatidylinositol metabolic process / Platelet degranulation / Clathrin-mediated endocytosis / cortical microtubule organization / vinculin binding / integrin activation / phosphatidylinositol biosynthetic process / cell-substrate junction assembly / cortical actin cytoskeleton organization / phosphatidylserine binding / regulation of postsynaptic neurotransmitter receptor internalization / exocytosis / regulation of synaptic vesicle endocytosis / phagocytosis / phagocytic cup / ruffle / phosphatidylinositol binding / axonogenesis / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / platelet aggregation / integrin binding / ruffle membrane / chemotaxis / actin filament binding / cytoskeleton / cell adhesion / endosome membrane / postsynaptic density / focal adhesion / glutamatergic synapse / cell surface / ATP binding / cytosol
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 / Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central ...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 / Talin VBS2 domain / 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 / Acyl-CoA Binding Protein - #10 / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Acyl-CoA Binding Protein / IRS-type PTB domain / PTB domain (IRS-1 type) / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Authorsde Pereda, J.M. / Wegener, K. / Santelli, E. / Bate, N. / Ginsberg, M.H. / Critchley, D.R. / Campbell, I.D. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural bases for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions
Authors: de Pereda, J.M. / Wegener, K. / Santelli, E. / Bate, N. / Ginsberg, M.H. / Critchley, D.R. / Campbell, I.D. / Liddington, R.C.
History
DepositionNov 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2016Group: Other
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
B: Talin 1
C: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
D: Talin 1
E: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
F: Talin 1
G: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
H: Talin 1
I: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
J: Talin 1
K: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
L: Talin 1


Theoretical massNumber of molelcules
Total (without water)149,96312
Polymers149,96312
Non-polymers00
Water8,395466
1
A: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
B: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
D: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
F: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
H: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
J: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma
L: Talin 1


Theoretical massNumber of molelcules
Total (without water)24,9942
Polymers24,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.102, 118.102, 93.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32

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Components

#1: Protein/peptide
Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma


Mass: 1711.829 Da / Num. of mol.: 6 / Fragment: C-TERMINAL REGION
Source method: isolated from a genetically manipulated source
Details: chimera of chain A/B, C/D, E/F, G/H, I/J, K/L / Source: (gene. exp.) Mus musculus (house mouse) / Description: FORMS CHIMERA WITH TALIN AT THE N-TERMINUS / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O70161
#2: Protein
Talin 1


Mass: 23281.965 Da / Num. of mol.: 6 / Fragment: F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN
Source method: isolated from a genetically manipulated source
Details: chimera of chain A/B, C/D, E/F, G/H, I/J, K/L / Source: (gene. exp.) Mus musculus (house mouse)
Description: FORMS CHIMERA WITH PHOSPHATIDYL INOSITOL KINASE TYPE 1 GAMMA AT THE C-TERMINUS
Gene: Tln1, Tln / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26039
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.2
Details: 0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 43284 / % possible obs: 96.7 % / Observed criterion σ(I): -4 / Redundancy: 2.4 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.4 / % possible all: 84.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2175 5 %OBEYS P622 SYMMETRY
Rwork0.253 ---
obs0.253 43146 96.5 %-
all-50362 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.526 Å2-6.955 Å20 Å2
2---4.526 Å20 Å2
3---9.052 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9882 0 0 466 10348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.06
X-RAY DIFFRACTIONc_mcbond_it1.5461.5
X-RAY DIFFRACTIONc_mcangle_it2.6673
X-RAY DIFFRACTIONc_scbond_it3.273
X-RAY DIFFRACTIONc_scangle_it4.8615
LS refinement shellResolution: 2.6→2.69 Å /
RfactorNum. reflection
Rfree0.407 190
Rwork0.377 -

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