[English] 日本語
Yorodumi
- EMDB-1359: Atypical AAA+ subunit packing creates an expanded cavity for disa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1359
TitleAtypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
Map dataHsp104 deltaN 3D density map. Hexamer bound to ATPgammaS.
Sample
  • Sample: Hsp104 deltaN ATPgammaS
  • Organelle or cellular component: Hsp104 deltaN
  • Em label: ATPgammaS
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsWendler P / Shorter J / Plisson C / Cashikar AG / Lindquist S / Saibil HR
CitationJournal: Cell / Year: 2007
Title: Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
Authors: Petra Wendler / James Shorter / Celia Plisson / Anil G Cashikar / Susan Lindquist / Helen R Saibil /
Abstract: Hsp104, a yeast protein-remodeling factor of the AAA+ (ATPases associated with various cellular activities) superfamily, and its homologs in bacteria and plants mediate cell recovery after severe ...Hsp104, a yeast protein-remodeling factor of the AAA+ (ATPases associated with various cellular activities) superfamily, and its homologs in bacteria and plants mediate cell recovery after severe stress by disaggregating denatured proteins through a poorly understood mechanism. Here, we present cryo-electron microscopy maps and domain fitting of Hsp104 hexamers, revealing an unusual arrangement of AAA+ modules with the prominent coiled-coil domain intercalated between the AAA+ domains. This packing results in a greatly expanded cavity, which is capped at either end by N- and C-terminal domains. The fitted structures as well as mutation of conserved coiled-coil arginines suggest that the coiled-coil domain plays a major role in the extraction of proteins from aggregates, providing conserved residues for key functions in ATP hydrolysis and potentially for substrate interaction. The large cavity could enable the uptake of polypeptide loops without a requirement for exposed N or C termini.
History
DepositionMay 16, 2007-
Header (metadata) releaseMay 16, 2007-
Map releaseJan 3, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1359.gif

Downloads & links

-
Map

FileDownload / File: emd_1359.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp104 deltaN 3D density map. Hexamer bound to ATPgammaS.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 128 pix.
= 358.4 Å		2.8 Å/pix.
x 128 pix.
= 358.4 Å		2.8 Å/pix.
x 128 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.377 / Movie #1: 0.2
Minimum - Maximum-2.208 - 10.0
Average (Standard dev.)0.0151339 (±0.240575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-63-64
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-63-64-64
NC/NR/NS128128128
D min/max/mean-2.20810.0000.015

-
Supplemental data

-
Sample components

-
Entire : Hsp104 deltaN ATPgammaS

EntireName: Hsp104 deltaN ATPgammaS
Components
  • Sample: Hsp104 deltaN ATPgammaS
  • Organelle or cellular component: Hsp104 deltaN
  • Em label: ATPgammaS

-
Supramolecule #1000: Hsp104 deltaN ATPgammaS

SupramoleculeName: Hsp104 deltaN ATPgammaS / type: sample / ID: 1000 / Oligomeric state: Hexamer / Number unique components: 2
Molecular weightExperimental: 500 KDa / Theoretical: 500 KDa

-
Supramolecule #1: Hsp104 deltaN

SupramoleculeName: Hsp104 deltaN / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Heat Shock Protein 104
Details: The Hsp104 fragment comprises aa residues 157 to 908.
Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightExperimental: 83 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pPROEX-HTb-Hsp104

-
Macromolecule #1: ATPgammaS

MacromoleculeName: ATPgammaS / type: em_label / ID: 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 20 mM NaCl, 10 mM MgCl2, 1mM DTT, 2mM ATPgammaS
GridDetails: 300 mesh copper grid- holey carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made
Method: The grids were blotted for 2-3 seconds and then immediately plunged into liquid ethane

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 77 K / Max: 85 K / Average: 77 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected for at 150,000 x magnification
DateJan 18, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 19 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.1 µm / Nominal magnification: 50000
Sample stageSpecimen holder: single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: phase flipping, each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 3623

-
Atomic model buiding 1

DetailsThe domains were fitted manually as rigid bodies using Pymol. Automated fitting in Chimera optimised the fit for NBD2.
RefinementProtocol: RIGID BODY FIT

+
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