[English] 日本語
Yorodumi
- PDB-1tbn: NMR STRUCTURE OF A PROTEIN KINASE C-G PHORBOL-BINDING DOMAIN, MIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tbn
TitleNMR STRUCTURE OF A PROTEIN KINASE C-G PHORBOL-BINDING DOMAIN, MINIMIZED AVERAGE STRUCTURE
ComponentsPROTEIN KINASE C, GAMMA TYPE
KeywordsCALCIUM-BINDING PROTEIN / PROTEIN KINASE C / PKC / TRANSFERASE
Function / homology
Function and homology information


Calmodulin induced events / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / calcium,diacylglycerol-dependent serine/threonine kinase activity / regulation of response to food / positive regulation of mismatch repair / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process ...Calmodulin induced events / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / calcium,diacylglycerol-dependent serine/threonine kinase activity / regulation of response to food / positive regulation of mismatch repair / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process / diacylglycerol-dependent serine/threonine kinase activity / innervation / regulation of phagocytosis / presynaptic cytosol / response to morphine / regulation of synaptic vesicle exocytosis / postsynaptic cytosol / response to pain / response to psychosocial stress / Trafficking of GluR2-containing AMPA receptors / calyx of Held / phosphorylation / negative regulation of protein ubiquitination / protein serine/threonine/tyrosine kinase activity / presynaptic modulation of chemical synaptic transmission / synaptic membrane / long-term synaptic potentiation / regulation of circadian rhythm / negative regulation of protein catabolic process / response to toxic substance / cell-cell junction / rhythmic process / presynapse / peptidyl-serine phosphorylation / chemical synaptic transmission / negative regulation of neuron apoptotic process / protein autophosphorylation / postsynaptic density / learning or memory / protein kinase activity / intracellular signal transduction / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / perinuclear region of cytoplasm / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, alpha/beta/gamma types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Protein kinase C, alpha/beta/gamma types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein kinase C gamma type / Protein kinase C gamma type
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodSOLUTION NMR / DG-SA
AuthorsXu, R.X. / Pawelczyk, T. / Xia, T. / Brown, S.C.
Citation
Journal: Biochemistry / Year: 1997
Title: NMR structure of a protein kinase C-gamma phorbol-binding domain and study of protein-lipid micelle interactions.
Authors: Xu, R.X. / Pawelczyk, T. / Xia, T.H. / Brown, S.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal Structure of the Cys2 Activator-Binding Domain of Protein Kinase C Delta in Complex with Phorbol Ester
Authors: Zhang, G. / Kazanietz, M.G. / Blumberg, P.M. / Hurley, J.H.
#2: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Solution Structure of Cysteine-Rich Domain of Protein Kinase C Alpha
Authors: Ichikawa, S. / Hatanaka, H. / Takeuchi, Y. / Ohno, S. / Inagaki, F.
#3: Journal: Nat.Struct.Biol. / Year: 1994
Title: Solution Structure of a Cysteine Rich Domain of Rat Protein Kinase C
Authors: Hommel, U. / Zurini, M. / Luyten, M.
History
DepositionApr 15, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,4903
Polymers9,3601
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1
Representative

-
Components

#1: Protein PROTEIN KINASE C, GAMMA TYPE / RAT BRAIN PKC-G


Mass: 9359.666 Da / Num. of mol.: 1 / Fragment: CYS2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: BRAIN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P05697, UniProt: P63319*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 6.5 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameClassification
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: DG-SA / Software ordinal: 1
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

+
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