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- EMDB-32947: Cryo-EM structure of human thioredoxin reductase bound by Au -

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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
KeywordsPROTEIN-METAL COMPLEX / HOMODIMERIC / OXIDOREDUCTASE / REDOX-ACTIVE CENTER / FAD
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 / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / mesoderm formation / cell redox homeostasis / FAD binding / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytosol / cytoplasm
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
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-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32947.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 100 pix.
= 160. Å		1.6 Å/pix.
x 100 pix.
= 160. Å		1.6 Å/pix.
x 100 pix.
= 160. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Sample components

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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

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Supramolecule #1: THIOREDOXIN REDUCTASE 1

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

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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

UniProtKB: Thioredoxin reductase 1, cytoplasmic

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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

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Macromolecule #3: GOLD ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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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

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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

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