[English] 日本語
Yorodumi
- EMDB-32947: Cryo-EM structure of human thioredoxin reductase bound by Au -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32947
TitleCryo-EM structure of human thioredoxin reductase bound by Au
Map dataCryo-EM map of human thioredoxin reductase bound with Au
Sample
  • Complex: THIOREDOXIN REDUCTASE 1
    • Protein or peptide: Thioredoxin reductase 1, cytoplasmic
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: GOLD ION
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / mesoderm formation / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cellular response to oxidative stress / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHe ZS / Cao P / Cao SH / He B / Jiang HD / Gong Y / Gao XY
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21727817 China
National Natural Science Foundation of China (NSFC)U2067214 China
National Basic Research Program of China (973 Program)2021YFA1201004 China
CitationJournal: Nano Today / Year: 2022
Title: Au4 cluster inhibits human thioredoxin reductase activity via specifically binding of Au to Cys189
Authors: Du Z / He Z / Fan J / Huo Y / He B / Wang Y / Sun Q / Niu W / Zhao W / Zhao L / Cao P / Cao K / Xia D / Yuan Q / Liang XJ / Jiang H / Gong Y / Gao X
History
DepositionFeb 24, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32947.png

Downloads & links

-
Map

FileDownload / File: emd_32947.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of human thioredoxin reductase bound with Au
Voxel sizeX=Y=Z: 1.6 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.3971653 - 0.6123772
Average (Standard dev.)0.00070339045 (±0.018678345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 160.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : THIOREDOXIN REDUCTASE 1

EntireName: THIOREDOXIN REDUCTASE 1
Components
  • Complex: THIOREDOXIN REDUCTASE 1
    • Protein or peptide: Thioredoxin reductase 1, cytoplasmic
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: GOLD ION

-
Supramolecule #1: THIOREDOXIN REDUCTASE 1

SupramoleculeName: THIOREDOXIN REDUCTASE 1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Thioredoxin reductase 1, cytoplasmic

MacromoleculeName: Thioredoxin reductase 1, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: thioredoxin-disulfide reductase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.116836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKL GSNGPEDLPK SYDYDLIIIG GGSGGLAAAK EAAQYGKKVM VLDFVTPTPL GTRWGLGGTC VNVGCIPKKL MHQAALLGQ ALQDSRNYGW KVEETVKHDW DRMIEAVQNH IGSLNWGYRV ALREKKVVYE NAYGQFIGPH RIKATNNKGK E KIYSAERF ...String:
MWSHPQFEKL GSNGPEDLPK SYDYDLIIIG GGSGGLAAAK EAAQYGKKVM VLDFVTPTPL GTRWGLGGTC VNVGCIPKKL MHQAALLGQ ALQDSRNYGW KVEETVKHDW DRMIEAVQNH IGSLNWGYRV ALREKKVVYE NAYGQFIGPH RIKATNNKGK E KIYSAERF LIATGERPRY LGIPGDKEYC ISSDDLFSLP YCPGKTLVVG ASYVALECAG FLAGIGLDVT VMVRSILLRG FD QDMANKI GEHMEEHGIK FIRQFVPIKV EQIEAGTPGR LRVVAQSTNS EEIIEGEYNT VMLAIGRDAC TRKIGLETVG VKI NEKTGK IPVTDEEQTN VPYIYAIGDI LEDKVELTPV AIQAGRLLAQ RLYAGSTVKC DYENVPTTVF TPLEYGACGL SEEK AVEKF GEENIEVYHS YFWPLEWTIP SRDNNKCYAK IICNTKDNER VVGFHVLGPN AGEVTQGFAA ALKCGLTKKQ LDSTI GIHP VCAEVFTTLS VTKRSGASIL QAGCUG

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #3: GOLD ION

MacromoleculeName: GOLD ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: AU
Molecular weightTheoretical: 196.967 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2cfy

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 821334
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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