+Open data
-Basic information
Entry | Database: PDB / ID: 7x1r | ||||||||||||
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Title | Cryo-EM structure of human thioredoxin reductase bound by Au | ||||||||||||
Components | Thioredoxin reductase 1, cytoplasmic | ||||||||||||
Keywords | OXIDOREDUCTASE / PROTEIN-METAL COMPLEX / HOMODIMERIC / 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 / 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 ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / 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 / cell redox homeostasis / 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 | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | He, Z.S. / Cao, P. / Cao, S.H. / He, B. / Jiang, H.D. / Gong, Y. / Gao, X.Y. | ||||||||||||
Funding support | China, 3items
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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, X.J. / Jiang, H. / Gong, Y. / Gao, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x1r.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x1r.ent.gz | 139 KB | Display | PDB format |
PDBx/mmJSON format | 7x1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/7x1r ftp://data.pdbj.org/pub/pdb/validation_reports/x1/7x1r | HTTPS FTP |
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-Related structure data
Related structure data | 32947MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 56116.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TXNRD1, GRIM12, KDRF / Cell line (production host): HEK293F / Production host: Homo sapiens (human) References: UniProt: Q16881, thioredoxin-disulfide reductase #2: Chemical | #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: THIOREDOXIN REDUCTASE 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 821334 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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