[English] 日本語
Yorodumi
- PDB-2i9h: NMR solution structure of the reduced form of thioredoxin 1 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i9h
TitleNMR solution structure of the reduced form of thioredoxin 1 from yeast (Trx1)
ComponentsThioredoxin I
KeywordsOXIDOREDUCTASE / thioredoxin / yeast / oxireductase
Function / homology
Function and homology information


membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole ...membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / cell redox homeostasis / mitochondrial intermembrane space / protein transport / Golgi membrane / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle simulated annealing
AuthorsPinheiro, A.S. / Amorim, G.C. / Almeida, F.C.L. / Valente, A.P.
Citation
Journal: Proteins / Year: 2008
Title: NMR solution structure of the reduced form of thioredoxin 1 from Sacharomyces cerevisiae
Authors: Pinheiro, A.S. / Amorim, G.C. / Netto, L.E. / Almeida, F.C. / Valente, A.P.
#1: Journal: J.BIOMOL.NMR / Year: 2006
Title: (1)H, (13)C and (15)N Resonance Assignments for the Reduced Forms of Thioredoxin 1 and 2 from S. cerevisiae
Authors: Pinheiro, A.S. / Amorim, G.C. / Netto, L.E. / Almeida, F.C. / Valente, A.P.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 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: Thioredoxin I


Theoretical massNumber of molelcules
Total (without water)11,2451
Polymers11,2451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20020 structures for lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Thioredoxin I / Thioredoxin isoform 1 / TR-I / Thioredoxin 2 /


Mass: 11244.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TRX1, TRX2, YLR043C / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22217

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
3332D NOESY
141HNCA-J
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
113C/15N uniformly labeled, 20mM phosphate buffer pH 7.0, DTT 10mM, Sodium azide 3mM; 90% H2O, 10% D2O90% H2O/10% D2O
215N uniformly labeled, 20mM phosphate buffer pH 7.0, DTT 10mM, Sodium azide 3mM; 90% H2O, 10% D2O90% H2O/10% D2O
3unlabeled, 20mM phosphate buffer pH 7.0, DTT 10mM, Sodium azide 3mM; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM phosphate 7.0 ambient 298 K
220 mM phosphate 7.0 ambient 298 K
320 mM phosphate 7.0 ambient 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle simulated annealing / Software ordinal: 1 / Details: cartesian simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 200 / 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://pdbjlvh1.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