[English] 日本語
Yorodumi
- PDB-1gmi: Structure of the c2 domain from novel protein kinase C epsilon -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gmi
TitleStructure of the c2 domain from novel protein kinase C epsilon
ComponentsPROTEIN KINASE C, EPSILON TYPE
KeywordsKINASE / PKC / C2 DOMAIN / PHOSPHOLIPIDS / PKC EPSILON.
Function / homology
Function and homology information


: / DAG and IP3 signaling / ethanol binding / SHC1 events in ERBB2 signaling / TRAM-dependent toll-like receptor 4 signaling pathway / Role of phospholipids in phagocytosis / Effects of PIP2 hydrolysis / negative regulation of mitochondrial calcium ion concentration / toxin catabolic process / positive regulation of lipid catabolic process ...: / DAG and IP3 signaling / ethanol binding / SHC1 events in ERBB2 signaling / TRAM-dependent toll-like receptor 4 signaling pathway / Role of phospholipids in phagocytosis / Effects of PIP2 hydrolysis / negative regulation of mitochondrial calcium ion concentration / toxin catabolic process / positive regulation of lipid catabolic process / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / mucus secretion / regulation of insulin secretion involved in cellular response to glucose stimulus / macrophage activation involved in immune response / regulation of release of sequestered calcium ion into cytosol / cellular response to ethanol / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / insulin secretion / positive regulation of mucus secretion / response to morphine / synaptic transmission, GABAergic / positive regulation of actin filament polymerization / positive regulation of wound healing / cell-substrate adhesion / positive regulation of cytokinesis / signaling receptor activator activity / locomotory exploration behavior / negative regulation of mitochondrial membrane potential / regulation of lipid metabolic process / positive regulation of epithelial cell migration / actin monomer binding / presynaptic cytosol / cellular response to platelet-derived growth factor stimulus / protein serine/threonine kinase binding / 14-3-3 protein binding / T-tubule / presynaptic modulation of chemical synaptic transmission / negative regulation of protein ubiquitination / lipopolysaccharide-mediated signaling pathway / enzyme activator activity / positive regulation of synaptic transmission, GABAergic / cell periphery / establishment of localization in cell / neuromuscular junction / positive regulation of insulin secretion / SH3 domain binding / MAPK cascade / cellular response to prostaglandin E stimulus / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / Golgi membrane / signaling receptor binding / cell division / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / endoplasmic reticulum / Golgi apparatus / mitochondrion / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta 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) ...Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta 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 epsilon type
Similarity search - Component
Biological speciesRATTUS RATTUS (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsOchoa, W.F. / Garcia-Garcia, J. / Fita, I. / Corbalan-Garcia, S. / Verdaguer, N. / Gomez-Fernandez, J.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure of the C2 Domain from Novel Protein Kinase Cepsilon. A Membrane Binding Model for Ca(2+ )-Independent C2 Domains
Authors: Ochoa, W.F. / Garcia-Garcia, J. / Fita, I. / Corbalan-Garcia, S. / Verdaguer, N. / Gomez-Fernandez, J.C.
History
DepositionSep 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN KINASE C, EPSILON TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2222
Polymers15,1981
Non-polymers241
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.300, 56.500, 60.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN KINASE C, EPSILON TYPE / PROTEIN KINASE C / NPKC-EPSILON


Mass: 15198.134 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS RATTUS (black rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09216
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.26 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.6
Details: 16% PEG8000, 0.1M HEPES PH=7.5, 0.2M MGCL2., pH 7.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
22 mg/mlDCPS1dropor DCPA
316 %(w/v)PEG80001reservoir
4100 mMHEPES1reservoir
50.2 M1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.993
DetectorDate: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 8248 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellHighest resolution: 1.7 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 15661 / % possible obs: 98 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.245

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Cross valid method: 15661 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.262 -10 %
Rwork0.234 --
obs0.234 15661 98 %
Solvent computationSolvent model: DM
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 1 107 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 10 /
Num. reflection% reflection
Rwork1400 -
obs-90 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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