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Yorodumi- EMDB-5476: Structure of the vacuolar-type ATPase from Saccharomyces cerevisi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5476 | |||||||||
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Title | Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11 Angstrom resolution | |||||||||
Map data | 3D map of V-type ATPase | |||||||||
Sample |
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Keywords | membrane protein / proton pump / ATPase / vacuole / endosome / lysosome / plasma membrane / Golgi | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | Benlekbir S / Bueler SA / Rubinstein JL | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2012 Title: Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution. Authors: Samir Benlekbir / Stephanie A Bueler / John L Rubinstein / Abstract: Vacuolar-type ATPases (V-type ATPases) in eukaryotic cells are large membrane protein complexes that acidify various intracellular compartments. The enzymes are regulated by dissociation of the V(1) ...Vacuolar-type ATPases (V-type ATPases) in eukaryotic cells are large membrane protein complexes that acidify various intracellular compartments. The enzymes are regulated by dissociation of the V(1) and V(O) regions of the complex. Here we present the structure of the Saccharomyces cerevisiae V-type ATPase at 11-Å resolution by cryo-EM of protein particles in ice. The structure explains many cross-linking and protein interaction studies. Docking of crystal structures suggests that inhibition of ATPase activity by the dissociated V(1) region involves rearrangement of the N- and C-terminal domains of subunit H and also suggests how this inhibition is triggered upon dissociation. We provide support for this model by demonstrating that mutation of subunit H to increase the rigidity of the linker between its two domains decreases its ability to inhibit ATPase activity. | |||||||||
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_5476.map.gz | 31.4 MB | EMDB map data format | |
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Header (meta data) | emd-5476-v30.xml emd-5476.xml | 50.3 KB 50.3 KB | Display Display | EMDB header |
Images | emd_5476_1.jpg | 43.4 KB | ||
Masks | emd_5476_msk_1.map emd_5476_msk_10.map emd_5476_msk_11.map emd_5476_msk_12.map emd_5476_msk_13.map emd_5476_msk_14.map emd_5476_msk_15.map emd_5476_msk_16.map emd_5476_msk_17.map emd_5476_msk_18.map emd_5476_msk_19.map emd_5476_msk_2.map emd_5476_msk_3.map emd_5476_msk_4.map emd_5476_msk_5.map emd_5476_msk_6.map emd_5476_msk_7.map emd_5476_msk_8.map emd_5476_msk_9.map | 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB 64 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5476 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5476 | HTTPS FTP |
-Validation report
Summary document | emd_5476_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
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Full document | emd_5476_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_5476_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5476 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5476 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5476.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of V-type ATPase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Segmentation: A subunit 2
+Segmentation: E subunit 3
+Segmentation: G subunit 1
+Segmentation: G subunit 2
+Segmentation: G subunit 3
+Segmentation: H subunit
+Segmentation: a subunit
+Segmentation: c-ring
+Segmentation: d subunit
+Segmentation: detergent/lipid plug
+Segmentation: A subunit 1
+Segmentation: A subunit 3
+Segmentation: B subunit 1
+Segmentation: B subunit 2
+Segmentation: B subunit 3
+Segmentation: C subunit
+Segmentation: DF subcomplex
+Segmentation: E subunit 1
+Segmentation: E subunit 2
-Sample components
-Entire : vacuolar-type ATPases
Entire | Name: vacuolar-type ATPases |
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Components |
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-Supramolecule #1000: vacuolar-type ATPases
Supramolecule | Name: vacuolar-type ATPases / type: sample / ID: 1000 Oligomeric state: A3B3CDE3FG3HadcXc'Yc''Z complex where X, Y, and Z indicate unknown stoichiometry Number unique components: 1 |
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Molecular weight | Experimental: 900 KDa / Theoretical: 900 KDa / Method: Gel filtration |
-Macromolecule #1: vacuolar-type ATPases
Macromolecule | Name: vacuolar-type ATPases / type: protein_or_peptide / ID: 1 / Name.synonym: V-ATPase / Details: Detergent solubilized protein complex / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SABY31 / synonym: Baker's yeast / Organelle: Intracellular membranes / Location in cell: Intracellular membranes |
Molecular weight | Experimental: 900 KDa / Theoretical: 900 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM Tris-HCl, 150 mM NaCl, 0.03% w/v dodecylmaltoside |
Grid | Details: Quantifoil R2/2 glow discharged in air |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 20 seconds before freezing |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Manually corrected by inspecting FFT |
Date | Jan 1, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 1000 / Average electron dose: 12 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | particles selected manually with Ximdisp |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: Search_Fspace, Refine_Fspace, Build_Fspace / Number images used: 34448 |