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Open data
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Basic information
Entry | Database: PDB / ID: 6ndy | ||||||||||||
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Title | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
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![]() | TRANSPORT PROTEIN/PEPTIDE / Vps4 / ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Han, H. / Fulcher, J.M. / Dandey, V.P. / Sundquist, W.I. / Kay, M.S. / Shen, P. / Hill, C.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281 KB | Display | ![]() |
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PDB format | ![]() | 229.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0443MC ![]() 6oo2C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 37120.750 Da / Num. of mol.: 5 / Fragment: residues 101-437 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 Production host: ![]() ![]() ![]() References: UniProt: P52917 #2: Protein/peptide | | Mass: 2660.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ADP / ![]() #4: Chemical | #5: Chemical | ChemComp-MG / Sequence details | The entry contains two cyclic peptides having the following sequences: ...The entry contains two cyclic peptides having the following sequences: GGDEIVNKVL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Vps4p-Cyclic Peptide complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Details: unspecified |
Vitrification![]() | Instrument: SPOTITON / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.5336 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
Image scans | Movie frames/image: 50 / Used frames/image: 2-50 |
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Processing
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction![]() | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237480 / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 3.6 Å |