+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-20142 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
![]() | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
![]() |
| ||||||||||||
![]() | Vps4 / ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Han H / Fulcher JM | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 49.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14 KB 14 KB | Display Display | ![]() |
Images | ![]() | 112.5 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oo2MC ![]() 0443C ![]() 6ndyC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Vps4-Vta1 with a Cyclic peptide binding to the central pore
Entire | Name: Vps4-Vta1 with a Cyclic peptide binding to the central pore |
---|---|
Components |
|
-Supramolecule #1: Vps4-Vta1 with a Cyclic peptide binding to the central pore
Supramolecule | Name: Vps4-Vta1 with a Cyclic peptide binding to the central pore type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 37.12075 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() |
-Macromolecule #2: Designed Cyclic Peptide
Macromolecule | Name: Designed Cyclic Peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
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: 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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 5.773649 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: TKDELTKIMD RASKIEQIQK LAKYAISALN YEDLPTAKDE LTKALDLLNS I UniProtKB: ![]() |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
---|---|
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 |
---|---|
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: 4 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 76.68 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER / Details: ab initio |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24778 |