[English] 日本語
Yorodumi
- PDB-3trx: HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3trx
TitleHIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINANT HUMAN THIOREDOXIN IN SOLUTION
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / protein-disulfide reductase (NAD(P)H) activity / positive regulation of peptidyl-cysteine S-nitrosylation / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / protein-disulfide reductase (NAD(P)H) activity / positive regulation of peptidyl-cysteine S-nitrosylation / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / positive regulation of DNA binding / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsForman-Kay, J.D. / Clore, G.M. / Gronenborn, A.M.
Citation
Journal: Biochemistry / Year: 1991
Title: High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution.
Authors: Forman-Kay, J.D. / Clore, G.M. / Wingfield, P.T. / Gronenborn, A.M.
#1: Journal: Biochemistry / Year: 1990
Title: Studies on the Solution Conformation of Human Thioredoxin Using Heteronuclear 15N-1H Nuclear Magnetic Resonance Spectroscopy
Authors: Forman-Kay, J.D. / Gronenborn, A.M. / Kay, L.E. / Wingfield, P.T. / Clore, G.M.
#2: Journal: Biochemistry / Year: 1989
Title: A Proton Nuclear Magnetic Resonance Assignment and Secondary Structure Determination of Recombinant Human Thioredoxin
Authors: Forman-Kay, J.D. / Clore, G.M. / Driscoll, P.C. / Wingfield, P. / Richards, F.M. / Gronenborn, A.M.
History
DepositionDec 17, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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_ref_seq_dif
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_ref_seq_dif.details
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: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,7201
Polymers11,7201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: RESIDUE PRO 75 IS A CIS PROLINE.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein THIOREDOXIN


Mass: 11720.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P10599

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Processing

RefinementSoftware ordinal: 1
Details: STRUCTURES DETERMINED BY THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD OF M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (FEBS LETT. 229, 317 (1988)). THE ...Details: STRUCTURES DETERMINED BY THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD OF M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (FEBS LETT. 229, 317 (1988)). THE STRUCTURES ARE BASED ON 1983 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 52 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 26 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; AND 98 PHI AND 71 PSI BACKBONE TORSION ANGLE RESTRAINTS AND 72 CHI1 SIDE-CHAIN TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS AND NOE DATA. A TOTAL OF 33 STRUCTURES WERE CALCULATED. THIS STRUCTURE REPRESENTS THE MINIMIZED AVERAGE STRUCTURE. THIS IS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE ENTIRE SET OF 33 STRUCTURES CAN BE FOUND IN PDB ENTRY 4TRX. THE LAST COLUMN IN THIS COORDINATE FILE REPRESENTS THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS.
NMR ensembleConformers 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