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- PDB-1vd2: Solution Structure of the PB1 domain of PKCiota -

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Basic information

Entry
Database: PDB / ID: 1vd2
TitleSolution Structure of the PB1 domain of PKCiota
ComponentsProtein kinase C, iota type
KeywordsTRANSFERASE / Kinase / PB1 domain / OPCA motif / aPKC / ZIP/p62 / MEK5 / molecular recognition
Function / homology
Function and homology information


Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / Schmidt-Lanterman incisure / membrane organization ...Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / Schmidt-Lanterman incisure / membrane organization / cellular response to chemical stress / positive regulation of endothelial cell apoptotic process / cell-cell junction organization / establishment or maintenance of epithelial cell apical/basal polarity / tight junction / protein targeting to membrane / intercellular bridge / positive regulation of Notch signaling pathway / cell leading edge / brush border / regulation of postsynaptic membrane neurotransmitter receptor levels / bicellular tight junction / vesicle-mediated transport / positive regulation of glial cell proliferation / cytoskeleton organization / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / actin filament organization / positive regulation of D-glucose import / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / phospholipid binding / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / cellular response to insulin stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / cell migration / positive regulation of NF-kappaB transcription factor activity / negative regulation of neuron apoptotic process / protein kinase activity / intracellular signal transduction / endosome / protein phosphorylation / apical plasma membrane / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Protein kinase C iota type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHirano, Y. / Yoshinaga, S. / Yokochi, M. / Ogura, K. / Noda, Y. / Sumimoto, H. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution structure of atypical protein kinase C PB1 domain and its mode of interaction with ZIP/p62 and MEK5
Authors: Hirano, Y. / Yoshinaga, S. / Ogura, K. / Yokochi, M. / Noda, Y. / Sumimoto, H. / Inagaki, F.
History
DepositionMar 18, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: Protein kinase C, iota type


Theoretical massNumber of molelcules
Total (without water)10,3221
Polymers10,3221
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 Protein kinase C, iota type


Mass: 10321.621 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKCiota / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P41743, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM PKCiota PB1 U-15N, U-13C; 50mM phosphate buffer; 150mM sodium chloride; 5mM ditiothreitol; 0.05%(w/v) sodium azide; 90% H2O, 10% D2O90% H2O/10% D2O
21mM PKCiota PB1 U-15N, U-13C; 50mM phosphate buffer; 150mM sodium chloride; 5mM ditiothreitol; 0.05%(w/v) sodium azide; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM phosphate buffer; 150mM sodium chloride
pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
VNMRcollection
NMRPipeprocessing
Oliviadata analysis
ARIAJ.P.Linge, S.I.O'Donoghue, M.Nilgesrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
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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