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- PDB-3qfb: Crystal structure of the human thioredoxin reductase-thioredoxin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qfb | ||||||
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Title | Crystal structure of the human thioredoxin reductase-thioredoxin complex | ||||||
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![]() | OXIDOREDUCTASE / Protein-Protein Complex / Rossmann Fold / Thioredoxin fold / homodimeric pyridine nucleotide disulfide oxidoreductase / electron transport | ||||||
Function / homology | ![]() Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / 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 / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / mesoderm formation / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / PPARA activates gene expression / fibrillar center / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K. | ||||||
![]() | ![]() Title: Crystal structure of the human thioredoxin reductase-thioredoxin complex Authors: Fritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.5 KB | Display | ![]() |
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PDB format | ![]() | 201 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 975 KB | Display | ![]() |
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Full document | ![]() | 1021 KB | Display | |
Data in XML | ![]() | 51.8 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qfaSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | THIOREDOXIN REDUCTASE DIMER (A, B) WITH EACH SUBUNIT COMPLEXED WITH ONE MOLECULE THIOREDOXIN (C or D) |
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Components
#1: Protein | Mass: 56925.805 Da / Num. of mol.: 2 / Mutation: C497S, U498C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16881, thioredoxin-disulfide reductase #2: Protein | Mass: 12992.681 Da / Num. of mol.: 2 / Mutation: C35S, C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE 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 SELENOCYST | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 15% PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 297.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 38660 / Num. obs: 38626 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.34 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.132 / Net I/σ(I): 11.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QFA Resolution: 2.6→49.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2189302.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.3104 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→49.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | 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 ...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 shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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