+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25790 | |||||||||
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Title | C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3 | |||||||||
Map data | Sharpened and masked C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3. This map has not had handedness inverted, as is shown in publication. | |||||||||
Sample |
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Keywords | oxygen scavenging / fmn / nadh / flavodiiron protein / OXIDOREDUCTASE | |||||||||
Biological species | Trichomonas vaginalis (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | Bell TA / Chao LH | |||||||||
Funding support | 2 items
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Citation | Journal: J Biol Chem / Year: 2022 Title: A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. Authors: Evana N Abdulaziz / Tristan A Bell / Bazlur Rashid / Mina L Heacock / Tarik Begic / Owen S Skinner / Mohammad A Yaseen / Luke H Chao / Vamsi K Mootha / Antonio J Pierik / Valentin Cracan / Abstract: Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. ...Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from HO-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: HO-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD while simultaneously removing O from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX-like enzyme and instead harbors three paralogous genes (FDPF1-3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a "stand-alone" FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25790.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-25790-v30.xml emd-25790.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25790_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_25790.png | 63.8 KB | ||
Filedesc metadata | emd-25790.cif.gz | 5 KB | ||
Others | emd_25790_additional_1.map.gz emd_25790_half_map_1.map.gz emd_25790_half_map_2.map.gz | 59.6 MB 49.7 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25790 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25790 | HTTPS FTP |
-Validation report
Summary document | emd_25790_validation.pdf.gz | 720.1 KB | Display | EMDB validaton report |
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Full document | emd_25790_full_validation.pdf.gz | 719.7 KB | Display | |
Data in XML | emd_25790_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_25790_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25790 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25790 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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EM raw data | EMPIAR-10895 (Title: C2-symmetric single-particle cryo-EM map of T. vaginalis FDPF3 - unaligned multi-frame micrographs Data size: 1.4 TB Data #1: Unaligned multi-frame micrographs of recombinantly expressed and purified T. vaginalis FDPF3 [picked particles - multiframe - unprocessed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25790.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened and masked C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3. This map has not had handedness inverted, as is shown in publication. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened, unmasked C1-symmetric single-particle cryo-EM map of T....
File | emd_25790_additional_1.map | ||||||||||||
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Annotation | Sharpened, unmasked C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3. This map has not had handedness inverted, as is shown in publication. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-class 1 from refinement prior to sharpening. This...
File | emd_25790_half_map_1.map | ||||||||||||
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Annotation | Half-class 1 from refinement prior to sharpening. This map has not had handedness inverted, as is shown in publication. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-class 2 from refinement prior to sharpening. This...
File | emd_25790_half_map_2.map | ||||||||||||
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Annotation | Half-class 2 from refinement prior to sharpening. This map has not had handedness inverted, as is shown in publication. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric assembly of TvFDPF3 N-terminal FDP-like domains
Entire | Name: Dimeric assembly of TvFDPF3 N-terminal FDP-like domains |
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Components |
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-Supramolecule #1: Dimeric assembly of TvFDPF3 N-terminal FDP-like domains
Supramolecule | Name: Dimeric assembly of TvFDPF3 N-terminal FDP-like domains type: complex / ID: 1 / Parent: 0 / Details: Resolved portion of full-lengh TvFDPF3 |
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Source (natural) | Organism: Trichomonas vaginalis (eukaryote) / Strain: C-1:NIH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.9 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting condition: 5 s at +15 blotting force.. | |||||||||
Details | Monodisperse sample |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7398 / Average electron dose: 54.5 e/Å2 / Details: Images were collected as 51-frame movies. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |