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- PDB-5w4s: Solution structure of C2 domain from protein kinase C alpha in te... -

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Basic information

Entry
Database: PDB / ID: 5w4s
TitleSolution structure of C2 domain from protein kinase C alpha in ternary complex with calcium and V5-pHM peptide
Components
  • Protein kinase C alpha type
  • V5-pHM peptide
KeywordsTRANSFERASE / phosphorylation
Function / homology
Function and homology information


Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ ...Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ / Syndecan interactions / positive regulation of angiotensin-activated signaling pathway / cellular response to carbohydrate stimulus / response to phorbol 13-acetate 12-myristate / positive regulation of dense core granule biogenesis / VEGFR2 mediated cell proliferation / cone photoreceptor outer segment / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / ooplasm / RET signaling / central nervous system neuron axonogenesis / desmosome assembly / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / regulation of platelet aggregation / positive regulation of macrophage differentiation / negative regulation of D-glucose import / regulation of muscle contraction / regulation of the force of heart contraction / induction of positive chemotaxis / alphav-beta3 integrin-PKCalpha complex / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of synapse assembly / response to corticosterone / muscle cell cellular homeostasis / positive regulation of cardiac muscle hypertrophy / regulation of synaptic vesicle exocytosis / Trafficking of GluR2-containing AMPA receptors / positive regulation of exocytosis / positive regulation of bone resorption / intercalated disc / peptidyl-threonine phosphorylation / positive regulation of blood vessel endothelial cell migration / response to mechanical stimulus / chondrocyte differentiation / presynaptic cytosol / negative regulation of MAPK cascade / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / presynaptic modulation of chemical synaptic transmission / positive regulation of endothelial cell migration / positive regulation of cell adhesion / positive regulation of mitotic cell cycle / response to interleukin-1 / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / calyx of Held / response to reactive oxygen species / histone H3T6 kinase activity / positive regulation of smooth muscle cell proliferation / stem cell differentiation / establishment of protein localization / mitochondrial membrane / response to peptide hormone / response to toxic substance / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of angiogenesis / integrin binding / apical part of cell / response to estradiol / angiogenesis / response to ethanol / learning or memory / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / cell adhesion / negative regulation of translation / intracellular signal transduction / ciliary basal body / positive regulation of cell migration / axon / signaling receptor binding / negative regulation of cell population proliferation / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / lipid binding / dendrite / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein-containing complex / mitochondrion / zinc ion binding
Similarity search - Function
Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYang, Y. / Igumenova, T.I.
Funding support United States, 3items
OrganizationGrant numberCountry
Welch FoundationA-1784 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108998 United States
National Science Foundation (NSF, United States)CHE-1151435 United States
CitationJournal: Biophys. J. / Year: 2018
Title: Structural Basis of Protein Kinase C alpha Regulation by the C-Terminal Tail.
Authors: Yang, Y. / Shu, C. / Li, P. / Igumenova, T.I.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C alpha type
B: V5-pHM peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6194
Polymers17,5392
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1710 Å2
ΔGint-31 kcal/mol
Surface area8580 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein kinase C alpha type / PKC-alpha


Mass: 16240.451 Da / Num. of mol.: 1 / Fragment: C2 domain residues 155-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkca, Pkca / Production host: Escherichia coli (E. coli) / References: UniProt: P05696, protein kinase C
#2: Protein/peptide V5-pHM peptide


Mass: 1298.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P05696*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic32D 1H-15N HSQC
232isotropic32D 1H-15N HSQC
141isotropic32D 1H-13C HSQC aliphatic
153isotropic12D 1H-13C HSQC aliphatic
163isotropic12D 1H-13C HSQC aromatic
1101isotropic33D C(CO)NH
191isotropic33D H(CCO)NH
181isotropic33D (H)CCH-TOCSY
173isotropic13D (H)CCH-COSY
1113isotropic13D aromatic (H)CCH-TOCSY
1123isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-15N NOESY
1141isotropic32D [F2-15N,13C filtered] NOESY
1153isotropic32D [F2-15N,13C filtered] NOESY
1161isotropic32D [F1,F2-15N,13C filtered] NOESY
2172isotropic32D [F1,F2-15N,13C filtered] NOESY
1181isotropic32D [F1,F2-15N,13C filtered] TOCSY
2192isotropic32D [F1,F2-15N,13C filtered] TOCSY
1201isotropic13D [F1-15N,13C filtered] 1H-15N NOESY
1213isotropic13D [F1-15N,13C filtered] 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 92% H2O/8% D2OThe C2 domain was isotopically enriched whereas the V5-pHM peptide is natural abundance. The V5-pHM peptide is in molar excess in this sample.V5-pHM excess92% H2O/8% D2O
solution23.75 mM CALCIUM ION, 1.47 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 0.6 mM V5-pHM peptide, 92% H2O/8% D2OThe C2 domain was isotopically enriched whereas the V5-pHM peptide is natural abundance. The C2 domain is in molar excess in this sample.C2 excess92% H2O/8% D2O
solution32.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 100% D2OThe C2 domain was isotopically enriched whereas the V5-pHM peptide is natural abundance. The V5-pHM peptide is in molar excess in this sample. Sample 1 was lyophilized and redissolved in D2O.V5-pHM excess D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.225 mMCALCIUM IONnatural abundance1
0.89 mMC2 domain of protein kinase C alpha[U-13C; U-15N]1
6.7 mMMESnatural abundance1
67 mMpotassium chloridenatural abundance1
0.2 mg/mLsodium azidenatural abundance1
2 mMV5-pHM peptidenatural abundance1
3.75 mMCALCIUM IONnatural abundance2
1.47 mMC2 domain of protein kinase C alpha[U-13C; U-15N]2
6.7 mMMESnatural abundance2
67 mMpotassium chloridenatural abundance2
0.2 mg/mLsodium azidenatural abundance2
0.6 mMV5-pHM peptidenatural abundance2
2.225 mMCALCIUM IONnatural abundance3
0.89 mMC2 domain of protein kinase C alpha[U-13C; U-15N]3
6.7 mMMESnatural abundance3
67 mMpotassium chloridenatural abundance3
0.2 mg/mLsodium azidenatural abundance3
2 mMV5-pHM peptidenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.076 Mcondition_161 atm296.15 K
20.077 Mcondition_261 atm296.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001Cryoprobe
Bruker AVANCE IIIBrukerAVANCE III6002Cryoprobe
Bruker AVANCE IIIBrukerAVANCE III5003RT probe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
HADDOCKBonvinstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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