[English] 日本語
Yorodumi
- PDB-1dsy: C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dsy
TitleC2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE
ComponentsPROTEIN KINASE C, ALPHA TYPE
KeywordsTRANSFERASE / CALCIUM++ / PHOSPHOLIPID BINDING PROTEIN / CALCIUM-BINDING PROTEIN / PHOSPHATIDYLSERINE / PROTEIN KINASE C
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
PHOSPHATE ION / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsVerdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C.
CitationJournal: EMBO J. / Year: 1999
Title: Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine.
Authors: Verdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C.
History
DepositionJan 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)16,8715
Polymers16,2401
Non-polymers6314
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.8, 58.8, 91.7
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PROTEIN KINASE C, ALPHA TYPE


Mass: 16240.451 Da / Num. of mol.: 1 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P05696, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE


Mass: 455.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34NO10P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8K, POTASSIUM PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-8 mg/mlprotein1drop
225 mMcalcium chloride1drop
32 mMDCPS1drop
425 mM1dropCaCl2
520 %PEG80001reservoir
650 mMpotassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 5950 / Num. obs: 5610 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Num. unique all: 562 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 17072
Reflection shell
*PLUS
% possible obs: 95.1 %

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2327 416 random
Rwork0.1947 --
all-5969 -
obs-5432 -
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 32 39 1180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.667
X-RAY DIFFRACTIONc_angle_d2.899
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.233 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

+
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