+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8587 | |||||||||
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Title | AAA ATPase Vps4 hexamer in closed conformation | |||||||||
Map data | AAA ATPase Vps4 hexamer in closed conformation | |||||||||
Sample |
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Function / homology | Function and homology information ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / nucleus organization / endosomal transport / ATPase complex / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Su M / Guo EZ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2017 Title: Mechanism of Vps4 hexamer function revealed by cryo-EM. Authors: Min Su / Emily Z Guo / Xinqiang Ding / Yan Li / Jeffrey T Tarrasch / Charles L Brooks / Zhaohui Xu / Georgios Skiniotis / Abstract: Vps4 is a member of AAA ATPase (adenosine triphosphatase associated with diverse cellular activities) that operates as an oligomer to disassemble ESCRT-III (endosomal sorting complex required for ...Vps4 is a member of AAA ATPase (adenosine triphosphatase associated with diverse cellular activities) that operates as an oligomer to disassemble ESCRT-III (endosomal sorting complex required for transport III) filaments, thereby catalyzing the final step in multiple ESCRT-dependent membrane remodeling events. We used electron cryo-microscopy to visualize oligomers of a hydrolysis-deficient Vps4 (vacuolar protein sorting-associated protein 4) mutant in the presence of adenosine 5'-triphosphate (ATP). We show that Vps4 subunits assemble into an asymmetric hexameric ring following an approximate helical path that sequentially stacks substrate-binding loops along the central pore. The hexamer is observed to adopt an open or closed ring configuration facilitated by major conformational changes in a single subunit. The structural transition of the mobile Vps4 subunit results in the repositioning of its substrate-binding loop from the top to the bottom of the central pore, with an associated translation of 33 Å. These structures, along with mutant-doping experiments and functional assays, provide evidence for a sequential and processive ATP hydrolysis mechanism by which Vps4 hexamers disassemble ESCRT-III filaments. | |||||||||
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_8587.map.gz | 724.7 KB | EMDB map data format | |
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Header (meta data) | emd-8587-v30.xml emd-8587.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_8587.png | 163.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8587 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8587 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8587.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AAA ATPase Vps4 hexamer in closed conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 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 : Vps4
Entire | Name: Vps4 |
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Components |
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-Supramolecule #1: Vps4
Supramolecule | Name: Vps4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Vps4
Macromolecule | Name: Vps4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSTGDFLTKG IELVQKAIDL DTATQYEEAY TAYYNGLDYL MLALKYEKNP KSKDLIRAKF TEYLNRAEQL KKHLESEEAN AAKKSPSAG SGSNGGNKKI SQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF K GNRKPTSG ...String: MSTGDFLTKG IELVQKAIDL DTATQYEEAY TAYYNGLDYL MLALKYEKNP KSKDLIRAKF TEYLNRAEQL KKHLESEEAN AAKKSPSAG SGSNGGNKKI SQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF K GNRKPTSG ILLYGPPGTG KSYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDQVDALT GT RGEGESE ASRRIKTELL VQMNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPS VLT KEDYRT LGAMTEGYSG SDIAVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPS SPGDDGAIEM SWTDIEADEL KEPD LTIKD FLKAIKSTRP TVNEDDLLKQ EQFTRDFGQE GN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 8.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 3) |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: EAMN (ver. 2) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 99175 |