[English] 日本語
Yorodumi
- PDB-1wik: Solution Structure of the PICOT homology 2 domain of the mouse PK... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wik
TitleSolution Structure of the PICOT homology 2 domain of the mouse PKC-interacting cousin of thioredoxin protein
ComponentsThioredoxin-like protein 2
KeywordsELECTRON TRANSPORT / PICOT homology 2 domain / PICOT protein / thioredoxin like 2 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster binding / protein-disulfide reductase activity / protein kinase C binding / Z disc / cell cortex / intracellular iron ion homeostasis ...protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster binding / protein-disulfide reductase activity / protein kinase C binding / Z disc / cell cortex / intracellular iron ion homeostasis / dendrite / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the PICOT homology 2 domain of the mouse PKC-interacting cousin of thioredoxin protein
Authors: Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin-like protein 2


Theoretical massNumber of molelcules
Total (without water)11,8401
Polymers11,8401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Thioredoxin-like protein 2 / PKC-interacting cousin of thioredoxin / PKC-theta-interacting protein / PKCq-interacting protein


Mass: 11840.396 Da / Num. of mol.: 1 / Fragment: PICOT homology 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2410003E11 / Plasmid: P030421-03 / References: UniProt: Q9CQM9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

-
Sample preparation

DetailsContents: 0.65mM PICOT homology 2 domain U-13C,15N; 20mM d-Tris-HCl(pH6.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10%D2O
Solvent system: 90% H2O, 10% D20
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.8996Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / 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