[English] 日本語
Yorodumi- EMDB-1481: cryo electron microscopy structure of Vps4p AMPPNP-complexed tetr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1481 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | cryo electron microscopy structure of Vps4p AMPPNP-complexed tetradecamer | |||||||||
Map data | This is a 3D reconstruction of a Vps4p AMPPNP-complexed tetradecamer. The N-terminal MIT-domain is deleted. | |||||||||
Sample |
| |||||||||
Keywords | vacuolar protein sorting / AAA-ATPase / ESCRT / HIV / Vps | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Hartmann C / Chami M / Zachariae U / de Groot BL / Engel A / Gruetter MG | |||||||||
Citation | Journal: J Mol Biol / Year: 2008 Title: Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. Authors: Claudia Hartmann / Mohamed Chami / Ulrich Zachariae / Bert L de Groot / Andreas Engel / Markus G Grütter / Abstract: The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in ...The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in tumor suppression, apoptosis, and retrovirus budding. We present the first atomic structure of the nucleotide-free yeast His(6)DeltaNVps4p dimer and its AMPPNP (5'-adenylyl-beta,gamma-imidodiphosphate)-bound tetradecamer, derived from a cryo electron microscopy map. Vps4p dimers form two distinct heptameric rings and accommodate AAA cassettes in a head-to-head--not in a head-to-tail-fashion as in class II AAA-ATPases. Our model suggests a mechanism for disassembling ESCRT (endosomal sorting complex required for transport) complexes by movements of substrate-binding domains located at the periphery of the tetradecamer during ATP hydrolysis in one ring, followed by translocation through the central pore and ATP hydrolysis in the second ring. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1481.map.gz | 5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1481-v30.xml emd-1481.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | 1481.gif | 56.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1481 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1481 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1481.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | This is a 3D reconstruction of a Vps4p AMPPNP-complexed tetradecamer. The N-terminal MIT-domain is deleted. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : His-tagged Vps4p AAA-ATPase cassette
Entire | Name: His-tagged Vps4p AAA-ATPase cassette |
---|---|
Components |
|
-Supramolecule #1000: His-tagged Vps4p AAA-ATPase cassette
Supramolecule | Name: His-tagged Vps4p AAA-ATPase cassette / type: sample / ID: 1000 / Details: fresh prepared / Oligomeric state: tetradecamer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 512 KDa / Theoretical: 512 KDa / Method: cryo electron microscopy |
-Macromolecule #1: Vps4p
Macromolecule | Name: Vps4p / type: protein_or_peptide / ID: 1 / Name.synonym: Vps4p / Number of copies: 14 / Oligomeric state: tetradecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: bakers' yeast / Location in cell: cytosol |
Molecular weight | Experimental: 512 KDa / Theoretical: 512 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pet20b |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 20 mM Tris |
Grid | Details: holey carbon film |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 97 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: home made Guillotine. add AMPPNP 15min before freezing. Use the Quantifoil holey carbone grids. Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Cryholder Gatan 626, / Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 97 K / Max: 97 K / Average: 97 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism corrected at 50 000 Legacy - Electron beam tilt params: no tilt |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 10 µm / Number real images: 80 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
-Image processing
CTF correction | Details: ctftilt, SPIDER |
---|---|
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 2473 |
Details | boxer |