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Yeast Hsp104 N728A ATPgS
in 'single particle' state, at 13 A resolution
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Entry
Database / IDEM DATA BANK (EMDB) / 1358
Sample Name / Map AnnotationYeast Hsp104 N728A ATPgS
Yeast Hsp104 N728A 3D density map. ATPgammaS bound hexamer.
AuthorsWendler P, Shorter J, Plisson C, Cashikar AG, Lindquist S, Saibil HR
Movies
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Related Entries
EMDB-1359
EMDB-1359
Cite

Cite: data citing same article

Last Update2007-05-16
Map Release Date2008-01-03
EMDB SitesEMDB @EBI (EU) EMDB @RCSB (USA)
Article
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
AffiliationDepartment of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.
ChemicalsFungal Proteins, Heat-Shock Proteins, Protein Subunits, Solutions, Adenosine Triphosphate (56-65-5), Arginine (74-79-3), Metalloendopeptidases (EC 3.4.24.-), m-AAA proteases (EC 3.4.24.-)
KeywordsAdenosine Triphosphate, Amino Acid Sequence, Arginine, Conserved Sequence, Cryoelectron Microscopy, Fungal Proteins, Heat-Shock Proteins, Imaging, Three-Dimensional, Metalloendopeptidases, Models, Molecular, Mutation, Protein Binding, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits, Solutions
LinksPubMed: 18160044 PubMed Central: 2211523 DOI: 10.1016/j.cell.2007.10.047
Map
Fileemd_1358.map ( map file in CCP4 format, 8389 KB )
ProjectionsProjectionProjectionProjectionProjection
Density
Histogram
Contour Level
(movie #1):		0.5
Minimum: -1.37277
Maximum: 9.96507
Average: 0.03466
Standard dev.: -
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : -63 A -64 A -64 A
Limit : 64 A 63 A 63 A
Spacing : 128 A 128 A 128 A
Unit CellA = 358.400 A , B = 358.400 A , C = 358.400 A ,
alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees
Pixel SpacingX = 2.8 A , Y = 2.8 A , Z = 2.8 A
CCP4 map header infounder construction!
mapMAP
mode2
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
DetailsSPIDER input image = mirda_model_twoblob_017mc.spi
Created by IMAGIC: IMAGICimage =FULL017mmirc 16-05-20 11:12:50

Created by IMAGIC: CCP4 image= FULL017mmirc.ccp4 16-05-20 11:57:16
Annotation DetailsYeast Hsp104 N728A 3D density map. ATPgammaS bound hexamer.
Supplement
Sample
NameYeast Hsp104 N728A ATPgS
Aggregation State single particle 
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
MutantYes
Natural SourceCell Location: cytoplasm, nucleus
Engineered SourceExp System: E. coli
Vector: pNOTAG
Component #2: ligand - ATPgammaS
Scientific nameATPgammaS
MutantNo
Experiment
Sample Preparation
BufferDetails: 20 mM HEPES pH 7.5, 20 mM NaCl, 10 mM MgCl2, 1 mM DTT, 2mM ATPgS
Sample Conc: 0.3 mg/ml
pH: 7.5
Sample Support Details300 mesh copper grid- holey carbon film
Vitrification
Cryogen NameETHANE
Instrumenthome made
MethodThe grids were blotted for 2-3 sec and immediately plunged into liquid ethane
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 Scans
Number of Digital Images35
Sampling Size7 microns
Od Range1
Quant Bit Number8
ScannerZEISS SCAI
Processing
3D Reconstruction
Algorithmangular reconstitution, common lines
SoftwareImagic, Spider
CTF Correctionphase flipping, each particle
Resolution By Author13
Resolution MethodFSC at 0.5 cut-off
EM Data Set ( single particle )
Number of Projections7211
Atomic Model Fitting
Model #0
DetailsThe domains were manually fitted as rigid bodies using Pymol. Automated fitting in Chimera optimised fit for NBD2.
Download
Data from EMDB
Header Informationemd-1358.xml ( XML format, 6,757 byte )
Map Dataemd_1358.map.gz ( 309,258 byte )Details
FTP site (EMDB mirror)EMD-1358
Data from PDBj EM Navigator
movie #1
ASF format (for windows) ( 5,731,631 byte )
MOV format (for Mac) ( 5,685,900 byte )
FLV format (for web page) ( 5,743,120 byte )
Session file for UCSF-Chimera ( 20,052 byte )
movie #2
ASF format (for windows) ( 5,642,031 byte )
MOV format (for Mac) ( 5,633,216 byte )
FLV format (for web page) ( 5,726,126 byte )
Session file for UCSF-Chimera ( 20,411 byte )