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Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.

by single particle reconstruction, at 13 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.5, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1358
TitleAtypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
MapYeast Hsp104 N728A 3D density map. ATPgammaS bound hexamer.
SampleYeast Hsp104 N728A ATPgS
AuthorsWendler P, Shorter J, Plisson C, Cashikar AG, Lindquist S, Saibil HR
DateDeposition: 2007-05-16, Header release: 2007-05-16, Map release: 2008-01-03, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.5, Made by UCSF CHIMERA

Supplemental images

1358.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1359
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1602

EMDB-1359

EMDB-1599
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell, Vol. 131, Issue 7, Page 1366-77, Year 2007
TitleAtypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
AuthorsPetra Wendler, James Shorter, Celia Plisson, Anil G Cashikar, Susan Lindquist, Helen R Saibil
Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.
KeywordsAdenosine Triphosphate (metabolism, 56-65-5), Amino Acid Sequence, Arginine (chemistry, 74-79-3), Conserved Sequence, Cryoelectron Microscopy, Fungal Proteins (chemistry), Heat-Shock Proteins (chemistry), Imaging, Three-Dimensional, Metalloendopeptidases (chemistry, 3.4.24.-), Models, Molecular, Mutation, Protein Binding, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits (chemistry), Solutions, m-AAA proteases (3.4.24.-)
LinksPII: S0092-8674(07)01400-6, DOI: 10.1016/j.cell.2007.10.047, PubMed: 18160044, PMC: PMC2211523
Map
FileEMD-1358.map ( map file in CCP4 format, 8389 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.57, 0.5 (movie #1):
Minimum - Maximum: -1.37277 - 9.96507
Average (Standard dev.): 0.0346584 (0.356831)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : -63 -64 -64
Limit : 64 63 63
Spacing : 128 128 128
Unit CellA = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.8 A , Y = 2.8 A , Z = 2.8 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-63-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ-63-64-64
NC,NX/NR,NY/NS,NZ128128128
D min/max/mean-1.3739.9650.035
Annotation DetailsYeast Hsp104 N728A 3D density map. ATPgammaS bound hexamer.
Supplement
Images
Images

1358.gif
Sample
NameYeast Hsp104 N728A ATPgS
Oligomeric Statehexamer
Number of Components2
Experimental Mass0.6 MDa
Theoretical Mass0.612 MDa
Mass-estimation MethodGel filtration Glutaraldehyde cross-linking
Component #1: protein - Heat Shock Protein 104
Scientific nameHsp104 N728A
Common NameHeat Shock Protein 104
Theoretical Mass0.1 MDa
Experimental Mass0.102 MDa
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesYeast
Recombinant expressionYes
Natural SourceCell Location: cytoplasm, nucleus
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Vector: pNOTAG
Component #2: ligand - ATPgammaS
Scientific nameATPgammaS
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc0.3 mg/ml
Specimen Support Details300 mesh copper grid- holey carbon film
Specimen Stateparticle
BufferDetails: 20 mM HEPES pH 7.5, 20 mM NaCl, 10 mM MgCl2, 1 mM DTT, 2mM ATPgS
pH: 7.5
Vitrification
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
MethodThe grids were blotted for 2-3 sec and immediately plunged into liquid ethane
DetailsVitrification instrument: home made
Imaging
MicroscopeFEI TECNAI F20
Date2005-03-17
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
Astigmatismobjective lens astigmatism was corrected for at
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1400 nm - 3900 nm
Specimen Holder
Holdersingle tilt cryo ( GATAN LIQUID NITROGEN )
Temperature77 Kelvin ( 77 Kelvin - 85 Kelvin )
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images35
Sampling Size7 microns
Od Range1
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmangular reconstitution, common lines
SoftwareImagic, Spider
CTF Correctionphase flipping, each particle
Resolution By Author13
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections7211
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
DetailsThe domains were manually fitted as rigid bodies using Pymol. Automated fitting in Chimera optimised fit for NBD2.
Download
Data from EMDB
Header (meta data in XML format)emd-1358.xml (8.4 KB)
Map dataemd_1358.map.gz (301.9 KB)
Images1358.gif (166.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1358
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 19.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 19.9 KB