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The Saccharomyces cerevisiae 26S proteasome at subnanometer resolution

by single particle reconstruction, at 9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1992
TitleThe Saccharomyces cerevisiae 26S proteasome at subnanometer resolution
Map26 proteasome
Sample26S Proteasome
Keywords26S, 19S, proteasome, regulatory particle, ubiquitin recognition, deubiquitination, AAA-ATPase
AuthorsLander GC, Estrin E, Matyskiela M, Bashore C, Nogales E, Martin A
DateDeposition: 2011-11-18, Header release: 2012-01-06, Map release: 2012-01-06, Last update: 2012-02-03
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNature, Vol. 482, Issue 7384, Page 186-91, Year 2012
TitleComplete subunit architecture of the proteasome regulatory particle.
AuthorsGabriel C Lander, Eric Estrin, Mary E Matyskiela, Charlene Bashore, Eva Nogales, Andreas Martin
Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA.
KeywordsAdenosine Triphosphatases (metabolism, 3.6.1.-), Adenosine Triphosphate (metabolism), Binding Sites, Endopeptidases (metabolism, 3.4.-), Escherichia coli (metabolism), Holoenzymes (chemistry), Models, Molecular, Proteasome Endopeptidase Complex (chemistry, 3.4.25.1), Protein Binding, Protein Conformation, Protein Subunits (chemistry), RPN1 protein, S cerevisiae, RPN11 protein, S cerevisiae, RPN2 protein, S cerevisiae, Recombinant Proteins (chemistry), Saccharomyces cerevisiae (enzymology), Saccharomyces cerevisiae Proteins (metabolism), Ubiquitin (metabolism)
LinksDOI: 10.1038/nature10774, PubMed: 22237024, PMC: PMC3285539
Map
Fileemd_1992.map.gz ( map file in CCP4 format, 65537 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2.17 A/pix
= 555.52 A
256 pix
2.17 A/pix
= 555.52 A
256 pix
2.17 A/pix
= 555.52 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum: -21.592 - 33.7328
Average (Standard dev.): 0.0686551 (1.12869)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin161616
Limit271271271
Spacing256256256
Unit CellA= B= C: 555.52 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.17 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.172.172.17
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z555.520555.520555.520
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS161616
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-21.59233.7330.069
Annotation Details26 proteasome
Supplement
Images
Images
Sample
Name26S Proteasome
Number of Components1
Oligomeric Stateholoenzyme
Theoretical Mass1.5MDa
Detailsmonodisperse
Mass-estimation MethodMass Spectrometry
Experimental Mass1.5MDa
Component #1: protein - 26S Proteasome
Scientific name26S Proteasome
Theoretical Mass1.5 MDa
Experimental Mass1.5 MDa
DetailsEndogenous proteasome was purified from yeast
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesYeast
NCBI taxonomy4932
StrainYYS40
Recombinant expressionNo
LinksInter Pro: IPR:001353, Gene Ontology: GO:0005838
Experiment
Sample Preparation
StainingC-flat grids made hydrophilic with Solarus Plasma cleaner, 4 uL of sample applied, blotted in Vitrobot for 3 seconds with offset -1, plunged into liquid ethane
Specimen Conc1.7 mg/ml
Specimen Support Details400-mesh C-flats, 2um holes with 2um spacing (Protochips Inc.)
Specimen Stateparticle
BufferDetails: 20mM HEPES, 50mM NaCl, 50mM KCl, 1mM ATP, 1mM DTT, 0.05% NP40
pH: 7.6
Vitrification
MethodBlot 3 seconds with -2 offset
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature86 Kelvin
Imaging
MicroscopeFEI TECNAI 20
Date11-SEP-2011
DetailsData acquired using Leginon
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000
Astigmatismobjective lens astigmatism was corrected at 210,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus1200 nm - 2600 nm
Specimen Holder
HolderSide-entry cryostage
ModelGATAN LIQUID NITROGEN
Temperature78 K ( 78 - 78 K)
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
#1
Number of Digital Images9153
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareEMAN2 SPARX
CTF Correctionwhole micrograph
DetailsFinal map filtered to local resolution using the blocfilt function in Bsoft
Resolution By Author9 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections93679
DetailsImage processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Applied SymmetryC2 (2 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1992.xml (8.1 KB)
Map dataemd_1992.map.gz (2.8 MB)
Imagesemd-1992.png (199.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1992
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.7 KB