+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0443 | ||||||||||||
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Title | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
Map data | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
Sample |
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Keywords | Vps4 / ESCRT / Vta1 / AAA ATPase / TRANSPORT PROTEIN / TRANSPORT PROTEIN-PEPTIDE complex | ||||||||||||
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) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Han H / Fulcher JM | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2019 Title: Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. Authors: Han Han / James M Fulcher / Venkata P Dandey / Janet H Iwasa / Wesley I Sundquist / Michael S Kay / Peter S Shen / Christopher P Hill / Abstract: Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single ...Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains. | ||||||||||||
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_0443.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-0443-v30.xml emd-0443.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_0443.png | 74.8 KB | ||
Filedesc metadata | emd-0443.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0443 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0443 | HTTPS FTP |
-Related structure data
Related structure data | 6ndyMC 6oo2C M: atomic model generated by this map C: citing same article (ref.) |
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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_0443.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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 : Vps4p-Cyclic Peptide complex
Entire | Name: Vps4p-Cyclic Peptide complex |
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Components |
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-Supramolecule #1: Vps4p-Cyclic Peptide complex
Supramolecule | Name: Vps4p-Cyclic Peptide complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 37.12075 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: QEEGEDNGGE DNKKLRGALS SAILSEKPNV KWEDVAGLEG AKEALKEAVI LPVKFPHLFK GNRKPTSGIL LYGPPGTGKS YLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ M NGVGNDSQ ...String: QEEGEDNGGE DNKKLRGALS SAILSEKPNV KWEDVAGLEG AKEALKEAVI LPVKFPHLFK GNRKPTSGIL LYGPPGTGKS YLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ M NGVGNDSQ GVLVLGATNI PWQLDSAIRR RFERRIYIPL PDLAARTTMF EINVGDTPCV LTKEDYRTLG AMTEGYSGSD IA VVVKDAL MQPIRKIQSA THFKDVSTED DETRKLTPCS PGDDGAIEMS WTDIEADELK EPDLTIKDFL KAIKSTRPTV NED DLLKQE QFTRDFGQEG N UniProtKB: Vacuolar protein sorting-associated protein 4 |
-Macromolecule #2: Designed Cyclic Peptide
Macromolecule | Name: Designed Cyclic Peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 2.66004 KDa |
Sequence | String: GGDEIVNKVL GGSSGG(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)GGKGCK |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / 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 | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: SPOTITON |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 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 QUANTUM (4k x 4k) / Digitization - Frames/image: 2-50 / Average exposure time: 0.2 sec. / Average electron dose: 1.5336 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 237480 |