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Yorodumi- EMDB-4111: Respiratory complex I of Yarrowia lipolytica with sulfur transfer... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4111 | |||||||||
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Title | Respiratory complex I of Yarrowia lipolytica with sulfur transferase subunit ST1 bound | |||||||||
Map data | Complex I from Yarrowia lipolyticsa with ST1 subunit bound | |||||||||
Sample |
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Biological species | Yarrowia lipolytica (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||
Authors | D'Imprima E / Mills DJ / Parey K / Brandt U / Kuehlbrandt W / Zickermann V / Vonck J | |||||||||
Citation | Journal: Biochim Biophys Acta / Year: 2016 Title: Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism. Authors: Edoardo D'Imprima / Deryck J Mills / Kristian Parey / Ulrich Brandt / Werner Kühlbrandt / Volker Zickermann / Janet Vonck / Abstract: Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved ...Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy. Our density map at 7.9Å resolution closely matches the 3.6-3.9Å X-ray structure of the Yarrowia lipolytica complex. However, the cryo-EM map indicated an additional subunit on the side of the matrix arm above the membrane surface, pointing away from the membrane arm. The density, which is not present in any previously described complex I structure and occurs in about 20 % of the particles, was identified as the accessory sulfur transferase subunit ST1. The Yarrowia lipolytica complex I preparation is active in generating HS from the cysteine derivative 3-mercaptopyruvate, catalyzed by ST1. We thus provide evidence for a link between respiratory complex I and mitochondrial sulfur metabolism. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4111.map.gz | 39.5 MB | EMDB map data format | |
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Header (meta data) | emd-4111-v30.xml emd-4111.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4111_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_4111.png | 57.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4111 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4111 | HTTPS FTP |
-Validation report
Summary document | emd_4111_validation.pdf.gz | 266.9 KB | Display | EMDB validaton report |
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Full document | emd_4111_full_validation.pdf.gz | 266.1 KB | Display | |
Data in XML | emd_4111_validation.xml.gz | 10.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4111 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4111 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4111.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Complex I from Yarrowia lipolyticsa with ST1 subunit bound | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : NADH:ubiquinone oxidoreductase
Entire | Name: NADH:ubiquinone oxidoreductase |
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Components |
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-Supramolecule #1: NADH:ubiquinone oxidoreductase
Supramolecule | Name: NADH:ubiquinone oxidoreductase / type: complex / ID: 1 / Parent: 0 Details: complex I with ST1 subunit bound to the peripheral arm |
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Source (natural) | Organism: Yarrowia lipolytica (yeast) |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: Before glow discharge the grids were pretreated in chloroform for 1-2 hrs | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: The samples were blotted for 8-10 seconds. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-24 / Number real images: 2250 / Average exposure time: 1.5 sec. / Average electron dose: 84.0 e/Å2 Details: Images were collected in movi-mode at 17 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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