+Open data
-Basic information
Entry | Database: PDB / ID: 6ndy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSPORT PROTEIN/PEPTIDE / Vps4 / ESCRT / Vta1 / AAA ATPase / TRANSPORT PROTEIN / TRANSPORT PROTEIN-PEPTIDE complex | ||||||||||||
Function / homology | Function and homology information ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vacuole organization / plasma membrane repair / membrane fission / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / nucleus organization / ATPase complex / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Han, H. / Fulcher, J.M. / Dandey, V.P. / Sundquist, W.I. / Kay, M.S. / Shen, P. / Hill, C.P. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ndy.cif.gz | 281 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ndy.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ndy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ndy_validation.pdf.gz | 1012.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ndy_full_validation.pdf.gz | 1022.9 KB | Display | |
Data in XML | 6ndy_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 6ndy_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/6ndy ftp://data.pdbj.org/pub/pdb/validation_reports/nd/6ndy | HTTPS FTP |
-Related structure data
Related structure data | 0443MC 6oo2C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Vps4p-Cyclic Peptide complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: SPOTITON / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |