+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8549 | |||||||||
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Title | Vps4-Vta1 complex | |||||||||
Map data | Vps4-Vta1 complex | |||||||||
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 / lipid transport / endosomal transport / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein-macromolecule adaptor activity / 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: 5.7 Å | |||||||||
Authors | Monroe N / Shen P / Han H / Sundquist WI / Hill CP | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2017 Title: Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase. Authors: Nicole Monroe / Han Han / Peter S Shen / Wesley I Sundquist / Christopher P Hill / Abstract: Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM ...Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeF, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 'walks' along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases. | |||||||||
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_8549.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-8549-v30.xml emd-8549.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_8549.png | 302 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8549 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8549 | HTTPS FTP |
-Related structure data
Related structure data | 5uieMC 8550C 8551C 8552C 8553C 8554C 8555C 8556C 8557C 8570C 8571C 8572C C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_8549.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Vps4-Vta1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.409 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-Vta1 complex
Entire | Name: Vps4-Vta1 complex |
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Components |
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-Supramolecule #1: Vps4-Vta1 complex
Supramolecule | Name: Vps4-Vta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 4
Macromolecule | Name: Vacuolar protein sorting-associated protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 48.233184 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 IFIDEVDALT GT RGEGESE ASRRIKTELL VQMNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPC VLT KEDYRT LGAMTEGYSG SDIAVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPC SPGDDGAIEM SWTDIEADEL KEPD LTIKD FLKAIKSTRP TVNEDDLLKQ EQFTRDFGQE GN |
-Macromolecule #2: DOA4-independent degradation protein 4
Macromolecule | Name: DOA4-independent degradation protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 724.891 Da |
Sequence | String: (ACE)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: Vacuolar protein sorting-associated protein VTA1
Macromolecule | Name: Vacuolar protein sorting-associated protein VTA1 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 37.35966 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS ...String: MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS SDEKTLDYAD FADDSEEIKD EDVDHQTSDL ENNNNDKVEG LAPKDQTTSY EPVDEVPEFI DDADSVNEEE QT VDKNEDA ITKDEQQVVK KEVDLTRPSA PSEPAAAEHK SYTKDELTKI MDRASKIEQI QKLAKYAISA LNYEDLPTAK DEL TKALDL LNSI |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.2 sec. / Average electron dose: 1.3 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / Details: e2initialmodel.py |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 58155 |