[English] 日本語
Yorodumi
- EMDB-5040: 3D structure of the ATP-bound yeast Vps4pE233Q dodecamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5040
Title3D structure of the ATP-bound yeast Vps4pE233Q dodecamer
Map data3D density map of ATP-bound yeast Vps4(delta)E233Q
Sample
  • Sample: 6xHis tagged yeast Vps4pE233Q
  • Protein or peptide: Vacuolar protein sorting 4
Keywordsprotein transport / AAA ATPase / endosomal sorting / enveloped virus budding
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsLandsberg MJ / Vajjhala PR / Rothnagel R / Munn AL / Hankamer B
CitationJournal: Structure / Year: 2009
Title: Three-dimensional structure of AAA ATPase Vps4: advancing structural insights into the mechanisms of endosomal sorting and enveloped virus budding.
Authors: Michael John Landsberg / Parimala Rao Vajjhala / Rosalba Rothnagel / Alan Leslie Munn / Ben Hankamer /
Abstract: Vps4 is a AAA ATPase that mediates endosomal membrane protein sorting. It is also a host factor hijacked by a diverse set of clinically important viruses, including HIV and Ebola, to facilitate viral ...Vps4 is a AAA ATPase that mediates endosomal membrane protein sorting. It is also a host factor hijacked by a diverse set of clinically important viruses, including HIV and Ebola, to facilitate viral budding. Here we present the three-dimensional structure of the hydrolysis-defective Vps4p(E233Q) mutant. Single-particle analysis, multiangle laser light scattering, and the docking of independently determined atomic models of Vps4 monomers reveal a complex with C6 point symmetry, distinguishing between a range of previously suggested oligomeric states (8-14 subunits). The 3D reconstruction also reveals a tail-to-tail subunit organization between the two rings of the complex and identifies the location of domains critical to complex assembly and interaction with partner proteins. Our refined Vps4 structure is better supported by independent lines of evidence than those previously proposed, and provides insights into the mechanism of endosomal membrane protein sorting and viral envelope budding.
History
DepositionDec 23, 2008-
Header (metadata) releaseOct 6, 2009-
Map releaseOct 6, 2009-
UpdateOct 6, 2009-
Current statusOct 6, 2009Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5040_1.png

Downloads & links

-
Map

FileDownload / File: emd_5040.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D density map of ATP-bound yeast Vps4(delta)E233Q
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.09 Å/pix.
x 96 pix.
= 392.352 Å		4.09 Å/pix.
x 96 pix.
= 392.352 Å		4.09 Å/pix.
x 96 pix.
= 392.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.5 / Movie #1: 3.2
Minimum - Maximum-8.311529999999999 - 13.5456
Average (Standard dev.)-0.00000000155219 (±0.826126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 392.352 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.0874.0874.087
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z392.352392.352392.352
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-8.31213.546-0.000

-
Supplemental data

-
Sample components

-
Entire : 6xHis tagged yeast Vps4pE233Q

EntireName: 6xHis tagged yeast Vps4pE233Q
Components
  • Sample: 6xHis tagged yeast Vps4pE233Q
  • Protein or peptide: Vacuolar protein sorting 4

-
Supramolecule #1000: 6xHis tagged yeast Vps4pE233Q

SupramoleculeName: 6xHis tagged yeast Vps4pE233Q / type: sample / ID: 1000 / Oligomeric state: The complex is a dodecamer / Number unique components: 1
Molecular weightExperimental: 560 KDa / Theoretical: 590 KDa / Method: Multi-angle laser light scattering

-
Macromolecule #1: Vacuolar protein sorting 4

MacromoleculeName: Vacuolar protein sorting 4 / type: protein_or_peptide / ID: 1 / Name.synonym: Vps4p(E233Q) / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Strain: Saccharomyces cerevisiae / Tissue: cytosol / Location in cell: Endosome membrame
Molecular weightExperimental: 560 KDa / Theoretical: 590 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET11a

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Details: 0.1M potassium acetate, 5mM magnesium acetate, 20mM Hepes, 1mM ATP
StainingType: NEGATIVE
Details: Grids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds.
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F30
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 93,000 times magnification
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 170 / Average electron dose: 60 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder: single tilt / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

DetailsParticles were selected semi-interactively using SwarmPS
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: IMAGIC, XMIPP, EMAN / Details: FSC at 0.5 cut-off estimates resolution at 18.3 / Number images used: 8590
Final two d classificationNumber classes: 340

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more