[English] 日本語
Yorodumi
- PDB-3qfa: Crystal structure of the human thioredoxin reductase-thioredoxin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qfa
TitleCrystal structure of the human thioredoxin reductase-thioredoxin complex
Components
  • Thioredoxin
  • Thioredoxin reductase 1, cytoplasmic
KeywordsOXIDOREDUCTASE / Protein-Protein Complex / Rossmann Fold / Thioredoxin fold / homodimeric pyridine nucleotide disulfide oxidoreductase / electron transport
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / Uptake and function of diphtheria toxin / mesoderm formation / protein-disulfide reductase activity / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / FAD binding / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / PPARA activates gene expression / fibrillar center / Oxidative Stress Induced Senescence / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin / Glutaredoxin / : / Glutaredoxin domain profile. / Thioredoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin / Glutaredoxin / : / Glutaredoxin domain profile. / Thioredoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site / Thioredoxin family active site. / Enolase-like; domain 1 / Thioredoxin domain profile. / FAD/NAD(P)-binding domain / Thioredoxin domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K.
CitationJournal: Nat Commun / Year: 2011
Title: Crystal structure of the human thioredoxin reductase-thioredoxin complex
Authors: Fritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin reductase 1, cytoplasmic
B: Thioredoxin reductase 1, cytoplasmic
C: Thioredoxin
D: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,96112
Polymers139,8374
Non-polymers2,1248
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-68 kcal/mol
Surface area47790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.250, 105.030, 120.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS ensembles :
ID
1
2
DetailsTHIOREDOXIN REDUCTASE DIMER (A, B) WITH EACH SUBUNIT COMPLEXED WITH ONE MOLECULE THIOREDOXIN (C or D)

-
Components

#1: Protein Thioredoxin reductase 1, cytoplasmic / TR / Gene associated with retinoic and interferon-induced mortality 12 protein / GRIM-12 / Gene ...TR / Gene associated with retinoic and interferon-induced mortality 12 protein / GRIM-12 / Gene associated with retinoic and IFN-induced mortality 12 protein / KM-102-derived reductase-like factor / Thioredoxin reductase TR1


Mass: 56925.805 Da / Num. of mol.: 2 / Mutation: C497S, U498C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIM12, KDRF, TXNRD1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q16881, thioredoxin-disulfide reductase (NADPH)
#2: Protein Thioredoxin / Trx / ATL-derived factor / ADF / Surface-associated sulphydryl protein / SASP


Mass: 12992.681 Da / Num. of mol.: 2 / Mutation: C35S, C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDX, TRX, TRX1, TXN / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P10599
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF ENTITY 1 BASED ON ISOFORM 5 OF DATABASE Q16881 (TRXR1_HUMAN). RESIDUE 498 IS ...THE SEQUENCE OF ENTITY 1 BASED ON ISOFORM 5 OF DATABASE Q16881 (TRXR1_HUMAN). RESIDUE 498 IS SELENOCYSTEINE IN THE DATABASE, AND AUTHOR STATED A MUTATION SECYS 498 CYS AT THIS POSITION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.15 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0068 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0068 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 84458 / Num. obs: 70734 / % possible obs: 83.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.096 / Net I/σ(I): 6.73

-
Processing

Software
NameClassification
MOSFLMdata reduction
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2j3n and 1aiu

2j3n

1aiu


Resolution: 2.2→24.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3192308.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3208 6 %RANDOM
Rwork0.237 ---
obs0.237 53469 84.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.8778 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å20 Å2
2--10.45 Å20 Å2
3----7.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9254 0 142 425 9821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.642.5
Refine LS restraints NCSNCS model details: NUMBER OF NCS GROUPS : 1. NCS GROUP : 1. NCS OPERATOR : 1. REFERENCE SELECTION: CHAIN A AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID ...NCS model details: NUMBER OF NCS GROUPS : 1. NCS GROUP : 1. NCS OPERATOR : 1. REFERENCE SELECTION: CHAIN A AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID 279:335 OR RESID 342:410 OR RESID 412:428 OR RESID 434:490). SELECTION : CHAIN B AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID 279:335 OR RESID 342:410 OR RESID 412:428 OR RESID 434:490)
Type: medium positional / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 533 6 %
Rwork0.32 8353 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fad.paramgol.top
X-RAY DIFFRACTION4gol.paramfad.top

+
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