[English] 日本語
Yorodumi
- PDB-2nce: Solution Structure of Ca2+-bound C2 domain from Protein Kinase C ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nce
TitleSolution Structure of Ca2+-bound C2 domain from Protein Kinase C alpha in the form of complex with V5-pHM peptide
ComponentsProtein kinase C alpha type
KeywordsTRANSFERASE
Function / homology
Function and homology information


response to phorbol 13-acetate 12-myristate / 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 phorbol 13-acetate 12-myristate / 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 / positive regulation of dense core granule biogenesis / VEGFR2 mediated cell proliferation / cone photoreceptor outer segment / ooplasm / RET signaling / central nervous system neuron axonogenesis / desmosome assembly / WNT5A-dependent internalization of FZD4 / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / RHO GTPases Activate NADPH Oxidases / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / regulation of platelet aggregation / positive regulation of macrophage differentiation / regulation of muscle contraction / regulation of the force of heart contraction / induction of positive chemotaxis / alphav-beta3 integrin-PKCalpha complex / negative regulation of D-glucose import / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of synapse assembly / response to corticosterone / muscle cell cellular homeostasis / regulation of synaptic vesicle exocytosis / positive regulation of cardiac muscle hypertrophy / Trafficking of GluR2-containing AMPA receptors / positive regulation of exocytosis / intercalated disc / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / negative regulation of MAPK cascade / positive regulation of bone resorption / presynaptic cytosol / response to mechanical stimulus / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / presynaptic modulation of chemical synaptic transmission / positive regulation of endothelial cell migration / calyx of Held / peptidyl-threonine phosphorylation / negative regulation of insulin receptor signaling pathway / positive regulation of cell adhesion / response to interleukin-1 / positive regulation of mitotic cell cycle / post-translational protein modification / intrinsic apoptotic signaling pathway / response to reactive oxygen species / stem cell differentiation / positive regulation of smooth muscle cell proliferation / 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 / histone H3T6 kinase activity / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / negative regulation of translation / cell adhesion / 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 / protein serine/threonine kinase activity / neuronal cell body / lipid binding / dendrite / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein-containing complex
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
Model detailslowest energy, model1
AuthorsYang, Y. / Igumenova, T.I.
CitationJournal: To be Published
Title: Ca2+-sensing domain contributes to auto-inhibition of protein kinase Calpha through interactions with C-terminal tail
Authors: Yang, Y. / Igumenova, T.I.
History
DepositionMar 28, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein kinase C alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3213
Polymers16,2401
Non-polymers802
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 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein kinase C alpha type / PKC-A / 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: 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-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D HN(CA)CB
1512D 1H-13C HSQC aliphatic
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D 1H-15N TOCSY
11112D 1H-13C HSQC aromatic
11213D (H)CCH-TOCSY aromatic
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11513D HNHA

-
Sample preparation

DetailsContents: 2.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2, 6.7 mM MES, 67 mM potassium chloride, 0.02 % sodium azide, 2 mM pHM peptide, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.225 mMCALCIUM ION-11
0.89 mMC2-2[U-13C; U-15N]1
6.7 mMMES-31
67 mMpotassium chloride-41
0.02 %sodium azide-51
2 mMpHM peptide-61
Sample conditionsIonic strength: 0.076 / pH: 6 / Pressure: ambient / Temperature: 296.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

-
Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionestructural validation
CcpNMRCCPNdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2689 / NOE intraresidue total count: 618 / NOE long range total count: 765 / NOE medium range total count: 250 / NOE sequential total count: 536 / Hydrogen bond constraints total count: 33 / Protein phi angle constraints total count: 105 / Protein psi angle constraints total count: 105
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