[English] 日本語
Yorodumi
- PDB-5w4s: Solution structure of C2 domain from protein kinase C alpha in te... -

+
Open data


ID or keywords:

Loading...

-
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 / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling ...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 / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ / positive regulation of angiotensin-activated signaling pathway / desmosome assembly / positive regulation of dense core granule biogenesis / histone H3T6 kinase activity / cone photoreceptor outer segment / regulation of receptor-mediated endocytosis / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / ooplasm / RET signaling / central nervous system neuron axonogenesis / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / cellular response to carbohydrate stimulus / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / regulation of muscle contraction / regulation of response to osmotic stress / positive regulation of macrophage differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / alphav-beta3 integrin-PKCalpha complex / regulation of the force of heart contraction / induction of positive chemotaxis / negative regulation of glucose import / presynaptic cytosol / positive regulation of synapse assembly / regulation of synaptic vesicle exocytosis / negative regulation of MAPK cascade / muscle cell cellular homeostasis / response to corticosterone / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / Trafficking of GluR2-containing AMPA receptors / calyx of Held / positive regulation of cell adhesion / intercalated disc / positive regulation of blood vessel endothelial cell migration / positive regulation of bone resorption / chondrocyte differentiation / response to mechanical stimulus / regulation of peptidyl-tyrosine phosphorylation / positive regulation of endothelial cell proliferation / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / response to interleukin-1 / positive regulation of endothelial cell migration / positive regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway / neutrophil chemotaxis / post-translational protein modification / ciliary basal body / negative regulation of protein phosphorylation / response to reactive oxygen species / stem cell differentiation / mitochondrial membrane / positive regulation of smooth muscle cell proliferation / peptidyl-threonine phosphorylation / establishment of protein localization / response to organic cyclic compound / response to toxic substance / response to peptide hormone / positive regulation of inflammatory response / intracellular calcium ion homeostasis / positive regulation of angiogenesis / integrin binding / apical part of cell / response to estradiol / angiogenesis / response to ethanol / cell population proliferation / learning or memory / negative regulation of translation / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / lipid binding / dendrite / perinuclear region of cytoplasm / enzyme 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 / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) ...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 / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
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

-
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_16.0 1 atm296.15 K
20.077 Mcondition_26.0 1 atm296.15 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more