+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32947 | ||||||||||||
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Title | Cryo-EM structure of human thioredoxin reductase bound by Au | ||||||||||||
Map data | Cryo-EM map of human thioredoxin reductase bound with Au | ||||||||||||
Sample |
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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 | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | He ZS / Cao P / Cao SH / He B / Jiang HD / Gong Y / Gao XY | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32947.map.gz | 558.8 KB | EMDB map data format | |
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Header (meta data) | emd-32947-v30.xml emd-32947.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_32947.png | 98.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32947 | HTTPS FTP |
-Validation report
Summary document | emd_32947_validation.pdf.gz | 331.2 KB | Display | EMDB validaton report |
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Full document | emd_32947_full_validation.pdf.gz | 330.7 KB | Display | |
Data in XML | emd_32947_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | emd_32947_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32947 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32947 | HTTPS FTP |
-Related structure data
Related structure data | 7x1rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32947.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map of human thioredoxin reductase bound with Au | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : THIOREDOXIN REDUCTASE 1
Entire | Name: THIOREDOXIN REDUCTASE 1 |
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Components |
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-Supramolecule #1: THIOREDOXIN REDUCTASE 1
Supramolecule | Name: THIOREDOXIN REDUCTASE 1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Thioredoxin reductase 1, cytoplasmic
Macromolecule | Name: Thioredoxin reductase 1, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: thioredoxin-disulfide reductase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 56.116836 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #3: GOLD ION
Macromolecule | Name: GOLD ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: AU |
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Molecular weight | Theoretical: 196.967 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied 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 assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |