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Yorodumi- EMDB-15084: cryo-EM structure of thioredoxin glutathione reductase in complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15084 | |||||||||
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Title | cryo-EM structure of thioredoxin glutathione reductase in complex with a non-competitive inhibitor | |||||||||
Map data | ||||||||||
Sample |
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Keywords | inhibitor / complex / flavoreductase / FLAVOPROTEIN | |||||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Schistosoma mansoni (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ardini M / Angelucci F / Fata F / Gabriele F / Effantin G / Ling W / Williams DL / Petukhova VZ / Petukhov PA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Non-covalent inhibitors of thioredoxin glutathione reductase with schistosomicidal activity in vivo. Authors: Valentina Z Petukhova / Sammy Y Aboagye / Matteo Ardini / Rachel P Lullo / Francesca Fata / Margaret E Byrne / Federica Gabriele / Lucy M Martin / Luke N M Harding / Vamshikrishna Gone / ...Authors: Valentina Z Petukhova / Sammy Y Aboagye / Matteo Ardini / Rachel P Lullo / Francesca Fata / Margaret E Byrne / Federica Gabriele / Lucy M Martin / Luke N M Harding / Vamshikrishna Gone / Bikash Dangi / Daniel D Lantvit / Dejan Nikolic / Rodolfo Ippoliti / Grégory Effantin / Wai Li Ling / Jeremy J Johnson / Gregory R J Thatcher / Francesco Angelucci / David L Williams / Pavel A Petukhov / Abstract: Only praziquantel is available for treating schistosomiasis, a disease affecting more than 200 million people. Praziquantel-resistant worms have been selected for in the lab and low cure rates from ...Only praziquantel is available for treating schistosomiasis, a disease affecting more than 200 million people. Praziquantel-resistant worms have been selected for in the lab and low cure rates from mass drug administration programs suggest that resistance is evolving in the field. Thioredoxin glutathione reductase (TGR) is essential for schistosome survival and a validated drug target. TGR inhibitors identified to date are irreversible and/or covalent inhibitors with unacceptable off-target effects. In this work, we identify noncovalent TGR inhibitors with efficacy against schistosome infections in mice, meeting the criteria for lead progression indicated by WHO. Comparisons with previous in vivo studies with praziquantel suggests that these inhibitors outperform the drug of choice for schistosomiasis against juvenile worms. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15084.map.gz | 94.8 MB | EMDB map data format | |
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Header (meta data) | emd-15084-v30.xml emd-15084.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15084_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_15084.png | 43.3 KB | ||
Others | emd_15084_additional_1.map.gz emd_15084_half_map_1.map.gz emd_15084_half_map_2.map.gz | 96 MB 95.8 MB 95.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15084 | HTTPS FTP |
-Validation report
Summary document | emd_15084_validation.pdf.gz | 709.8 KB | Display | EMDB validaton report |
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Full document | emd_15084_full_validation.pdf.gz | 709.4 KB | Display | |
Data in XML | emd_15084_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_15084_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15084 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15084 | HTTPS FTP |
-Related structure data
Related structure data | 8a1rMC 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_15084.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.145 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: This is the final sharpened map made by...
File | emd_15084_additional_1.map | ||||||||||||
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Annotation | This is the final sharpened map made by Phenix (version 1.19.2-4158) local anisotropic sharpening from the refined fullmap_handcoot_map.ccp4 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15084_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15084_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TGR in complex with an inhibitor
Entire | Name: TGR in complex with an inhibitor |
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Components |
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-Supramolecule #1: TGR in complex with an inhibitor
Supramolecule | Name: TGR in complex with an inhibitor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Recombinant TGR bound non-covalently to a synthetic chimeric compound |
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Source (natural) | Organism: Schistosoma mansoni (invertebrata) |
-Supramolecule #2: TGR complex with inhibitor
Supramolecule | Name: TGR complex with inhibitor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Schistosoma mansoni (invertebrata) |
-Macromolecule #1: Thioredoxin glutathione reductase
Macromolecule | Name: Thioredoxin glutathione reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ec: 1.6.4.5 |
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Source (natural) | Organism: Schistosoma mansoni (invertebrata) |
Molecular weight | Theoretical: 65.061145 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPPADGTSQW LRKTVDSAAV ILFSKTTCPY CKKVKDVLAE AKIKHATIEL DQLSNGSAIQ KCLASFSKIE TVPQMFVRGK FIGDSQTVL KYYSNDELAG IVNESKYDYD LIVIGGGSGG LAAGKEAAKY GAKTAVLDYV EPTPIGTTWG LGGTCVNVGC I PKKLMHQA ...String: MPPADGTSQW LRKTVDSAAV ILFSKTTCPY CKKVKDVLAE AKIKHATIEL DQLSNGSAIQ KCLASFSKIE TVPQMFVRGK FIGDSQTVL KYYSNDELAG IVNESKYDYD LIVIGGGSGG LAAGKEAAKY GAKTAVLDYV EPTPIGTTWG LGGTCVNVGC I PKKLMHQA GLLSHALEDA EHFGWSLDRS KISHNWSTMV EGVQSHIGSL NWGYKVALRD NQVTYLNAKG RLISPHEVQI TD KNQKVST ITGNKIILAT GERPKYPEIP GAVEYGITSD DLFSLPYFPG KTLVIGASYV ALECAGFLAS LGGDVTVMVR SIL LRGFDQ QMAEKVGDYM ENHGVKFAKL CVPDEIKQLK VVDTENNKPG LLLVKGHYTD GKKFEEEFET VIFAVGREPQ LSKV LCETV GVKLDKNGRV VCTDDEQTTV SNVYAIGDIN AGKPQLTPVA IQAGRYLARR LFAGATELTD YSNVATTVFT PLEYG ACGL SEEDAIEKYG DKDIEVYHSN FKPLEWTVAH REDNVCYMKL VCRKSDNMRV LGLHVLGPNA GEITQGYAVA IKMGAT KAD FDRTIGIHPT CSETFTTLHV TKKSGVSPIV SGCCG |
-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: (2~{R},3~{R},4~{S},5~{R})-2-[3-[[[(1~{R},2~{R},3~{R},5~{S})-2,6,6...
Macromolecule | Name: (2~{R},3~{R},4~{S},5~{R})-2-[3-[[[(1~{R},2~{R},3~{R},5~{S})-2,6,6-trimethyl-3-bicyclo[3.1.1]heptanyl]amino]methyl]indol-1-yl]oxane-3,4,5-triol type: ligand / ID: 3 / Number of copies: 2 / Formula: KW2 |
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Molecular weight | Theoretical: 414.538 Da |
Chemical component information | ChemComp-KW2: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: filtered aqueous fresh solution | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time= 7s, wait time= 10 s. | |||||||||
Details | Mono-dispersed TGR molecules in aqueous sample buffer containing DMSO and inhibitor |
-Electron microscopy
Microscope | TFS GLACIOS |
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Details | Manual preliminar screening |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2600 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 12000 |
Sample stage | Cooling holder cryogen: NITROGEN |