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Yorodumi- EMDB-2280: Negative stain EM structure of the HOPS tethering complex (confor... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2280 | |||||||||
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Title | Negative stain EM structure of the HOPS tethering complex (conformation 1) | |||||||||
Map data | Reconstruction of HOPS tethering complex | |||||||||
Sample |
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Keywords | vesicular transport / homotypic fusion / multisubunit tethering complex / Rab binding | |||||||||
Function / homology | Function and homology information histone catabolic process / organelle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / endosomal vesicle fusion / vesicle tethering / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / vacuolar protein processing ...histone catabolic process / organelle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / endosomal vesicle fusion / vesicle tethering / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / vacuolar protein processing / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / Golgi to vacuole transport / cytoplasm to vacuole targeting by the Cvt pathway / vesicle docking / protein targeting to vacuole / endosome organization / vacuole organization / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / fungal-type vacuole / vesicle docking involved in exocytosis / endosomal transport / fungal-type vacuole membrane / vesicle-mediated transport / positive regulation of TORC1 signaling / cellular response to starvation / guanyl-nucleotide exchange factor activity / macroautophagy / intracellular protein transport / RING-type E3 ubiquitin transferase / small GTPase binding / autophagy / endocytosis / ubiquitin protein ligase activity / protein transport / late endosome / early endosome membrane / protein-macromolecule adaptor activity / actin binding / endosome / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.4 Å | |||||||||
Authors | Broecker C / Kuhlee A / Gatsogiannis C / Balderhaar HJ / Hoenscher C / Engelbrecht-Vandre S / Ungermann C / Raunser S | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Molecular architecture of the multisubunit homotypic fusion and vacuole protein sorting (HOPS) tethering complex. Authors: Cornelia Bröcker / Anne Kuhlee / Christos Gatsogiannis / Henning J kleine Balderhaar / Carina Hönscher / Siegfried Engelbrecht-Vandré / Christian Ungermann / Stefan Raunser / Abstract: Membrane fusion within the eukaryotic endomembrane system depends on the initial recognition of Rab GTPase on transport vesicles by multisubunit tethering complexes and subsequent coupling to SNARE- ...Membrane fusion within the eukaryotic endomembrane system depends on the initial recognition of Rab GTPase on transport vesicles by multisubunit tethering complexes and subsequent coupling to SNARE-mediated fusion. The conserved vacuolar/lysosomal homotypic fusion and vacuole protein sorting (HOPS) tethering complex combines both activities. Here we present the overall structure of the fusion-active HOPS complex. Our data reveal a flexible ≈30-nm elongated seahorse-like structure, which can adopt contracted and elongated shapes. Surprisingly, both ends of the HOPS complex contain a Rab-binding subunit: Vps41 and Vps39. The large head contains in addition to Vps41 the SNARE-interacting Vps33, whereas Vps39 is found in the bulky tip of its tail. Vps11 and Vps18 connect head and tail. Our data suggest that HOPS bridges Ypt7-positive membranes and chaperones SNAREs at fusion sites. | |||||||||
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_2280.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-2280-v30.xml emd-2280.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | 2280-image1.png | 92 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2280 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2280 | HTTPS FTP |
-Validation report
Summary document | emd_2280_validation.pdf.gz | 190 KB | Display | EMDB validaton report |
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Full document | emd_2280_full_validation.pdf.gz | 189.1 KB | Display | |
Data in XML | emd_2280_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2280 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2280 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2280.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of HOPS tethering complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 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 : vacuole protein sorting (HOPS) tethering complex containing Vps11...
Entire | Name: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41 |
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Components |
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-Supramolecule #1000: vacuole protein sorting (HOPS) tethering complex containing Vps11...
Supramolecule | Name: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41 type: sample / ID: 1000 / Details: Vps39 is fused to GFP, Vps41 is fused to TAP-tag / Oligomeric state: Monomer / Number unique components: 6 |
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Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: vacuolar protein sorting-associated protein 41
Macromolecule | Name: vacuolar protein sorting-associated protein 41 / type: protein_or_peptide / ID: 1 / Name.synonym: FET2, VAM2, vps41 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: Vacuolar protein sorting-associated protein 41 / GO: HOPS complex |
-Macromolecule #2: vacuolar protein sorting-associated protein 39
Macromolecule | Name: vacuolar protein sorting-associated protein 39 / type: protein_or_peptide / ID: 2 / Name.synonym: VAM6,CVT4, VPL18, VPL22, vps39 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: Vacuolar morphogenesis protein 6 / GO: HOPS complex |
-Macromolecule #3: vacuolar protein sorting-associated protein 33
Macromolecule | Name: vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 3 Name.synonym: Protein SLP1, Vacuolar morphogenesis protein 5, vps33 Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: Vacuolar protein sorting-associated protein 33 / GO: HOPS complex |
-Macromolecule #4: vacuolar protein sorting-associated protein 18
Macromolecule | Name: vacuolar protein sorting-associated protein 18 / type: protein_or_peptide / ID: 4 / Name.synonym: PEP3, VAM8, VPT18, vps18 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: Vacuolar membrane protein PEP3 / GO: HOPS complex |
-Macromolecule #5: vacuolar protein sorting-associated protein 11
Macromolecule | Name: vacuolar protein sorting-associated protein 11 / type: protein_or_peptide / ID: 5 / Name.synonym: END1, VAM1, VPL9, VPS11, VPT11, YMR231W / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: E3 ubiquitin-protein ligase PEP5 / GO: HOPS complex |
-Macromolecule #6: vacuolar protein sorting-associated protein 16
Macromolecule | Name: vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 6 / Name.synonym: VAM9, VPT16 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Sequence | UniProtKB: Vacuolar protein sorting-associated protein 16 / GO: HOPS complex |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 1 M NaCl, 50 mM Hepes/NaOH, 10% glycerol |
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Staining | Type: NEGATIVE Details: Grids with adsorbed Protein floated on 0.07% Uranyl Formate for 1-3h at 4C. |
Grid | Details: glow discharged 400 mesh copper grids with thin carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1400 |
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Date | Feb 7, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm / Number real images: 920 / Average electron dose: 4.5 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 0.0017 µm / Nominal defocus min: 0.0013 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: JEOL |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 2979 |
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