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- PDB-2ju0: Structure of Yeast Frequenin bound to PdtIns 4-kinase -

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Basic information

Entry
Database: PDB / ID: 2ju0
TitleStructure of Yeast Frequenin bound to PdtIns 4-kinase
Components
  • Calcium-binding protein NCS-1
  • Phosphatidylinositol 4-kinase PIK1
KeywordsMETAL BINDING PROTEIN/SIGNALING PROTEIN / EF-hand / calcium / PtdIns 4-kinase / frequenin / yeast / Lipoprotein / Membrane / Myristate / Nucleus / Phosphorylation / Transferase / METAL BINDING PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


microlipophagy / cellular bud membrane / Inactivation, recovery and regulation of the phototransduction cascade / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the Golgi membrane / positive regulation of autophagosome assembly / positive regulation of Golgi to plasma membrane protein transport / cellular response to nitrogen starvation / phosphatidylinositol-mediated signaling ...microlipophagy / cellular bud membrane / Inactivation, recovery and regulation of the phototransduction cascade / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the Golgi membrane / positive regulation of autophagosome assembly / positive regulation of Golgi to plasma membrane protein transport / cellular response to nitrogen starvation / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of signal transduction / positive regulation of protein secretion / enzyme activator activity / trans-Golgi network / endocytosis / Golgi membrane / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1260 / Phosphatidylinositol 4-kinase, Pik1, fungi / Yeast phosphatidylinositol-4-OH kinase Pik1 / : / PI4KB/PIK1, accessory (PIK) domain / Recoverin family / EF hand domain / EF-hand domain pair / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain ...Helix Hairpins - #1260 / Phosphatidylinositol 4-kinase, Pik1, fungi / Yeast phosphatidylinositol-4-OH kinase Pik1 / : / PI4KB/PIK1, accessory (PIK) domain / Recoverin family / EF hand domain / EF-hand domain pair / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Helix Hairpins / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Armadillo-type fold / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase PIK1 / Calcium-binding protein NCS-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsAmes, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
Authors: Strahl, T. / Huttner, I.G. / Lusin, J.D. / Osawa, M. / King, D. / Thorner, J. / Ames, J.B.
History
DepositionAug 11, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Calcium-binding protein NCS-1
B: Phosphatidylinositol 4-kinase PIK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7895
Polymers27,6682
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Calcium-binding protein NCS-1


Mass: 22036.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FRQ1, NCS1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06389
#2: Protein Phosphatidylinositol 4-kinase PIK1 / PI4-kinase / PtdIns-4-kinase


Mass: 5631.423 Da / Num. of mol.: 1 / Fragment: Residues:121-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PIK1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P39104, 1-phosphatidylinositol 4-kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] Frq1, 0.5 mM Pik1, 10 mM sodium acetate, 1 mM [U-2H] DTT, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM Frq1, 0.5 mM [U-13C; U-15N] Pik1, 10 mM sodium acetate, 1 mM [U-2H] DTT, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMFrq1[U-13C; U-15N]1
0.5 mMPik11
10 mMsodium acetate1
1 mMDTT[U-2H]1
5 mMcalcium chloride1
0.5 mMFrq12
0.5 mMPik1[U-13C; U-15N]2
10 mMsodium acetate2
1 mMDTT[U-2H]2
5 mMcalcium chloride2
Sample conditionsIonic strength: 15 / pH: 5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: NMRPipe
Developer: Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
Classification: processing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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