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Negative stain reconstruction of the Saccharomyces cerevisiae proteasome lid

by single particle reconstruction, at 15 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 5, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 5, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1994
AuthorsLander GC, Estrin E, Matyskiela M, Bashore C, Nogales E, Martin A
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 5, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 5, Made by UCSF CHIMERA

Supplemental images

em1994.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1992
Cite

EMDB-1993
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Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1993

PDB-4a7h

PDB-4a7f

EMDB-5163

PDB-4a7l
List of similar structure data about Omokage system
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, 56-65-5), 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-1994.map ( map file in CCP4 format, 8390 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:5.0 (by author), 5 (movie #1):
Minimum - Maximum: -5.48156 - 17.3354
Average (Standard dev.): -5.82217e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : -64 -64 -64
Limit : 63 63 63
Spacing : 128 128 128
Unit CellA = 353.28 A , B = 353.28 A , C = 353.28 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.76 A , Y = 2.76 A , Z = 2.76 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.762.762.76
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z353.280353.280353.280
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.48217.335-0.000
Annotation Detailsmap of endogenous Saccharomyces cerevisiae proteasome lid
Supplement
Images
Images

em1994.png
Sample
NameSaccharomyces cerevisiae proteasome lid subcomplex
Number of Components1
Oligomeric State8 subunit complex
Theoretical Mass0.361 MDa
Detailsmonodisperse
Mass-estimation MethodMass Spectrometry
Experimental Mass0.361 MDa
Component #1: protein - lid
Scientific namelid
Theoretical Mass0.361 MDa
Experimental Mass0.361 MDa
Detailslid was purified from endogenous proteasome holoenzyme using a 1M salt wash
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBaker's Yeast
StrainYYS40
Recombinant expressionNo
LinksInterPro: IPR:002015, Gene Ontology: GO:0008541
Experiment
Sample Preparation
StainingProtein adsorbed to grid for 1 minute, then passed over four 50uL drops of 2% w/v uranyl formate, 5 seconds on each drop
Specimen Conc0.009 mg/ml
Specimen Support Details200 mesh Cu grid
Specimen Stateparticle
BufferDetails: 60mM HEPES, 50mM NaCl, 50mM KCl, 5 mM MgCl2, 0.5mM EDTA, 1mM DTT, 10% glycerol
pH: 7.6
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 20
Date02-APR-2011
DetailsData acquired using Leginon
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000 X, Calibrated: 80000 X
Astigmatismobjective lens astigmatism was corrected at 210,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus500 nm - 1200 nm
Specimen Holder
HolderRoom temp single tilt ( SIDE ENTRY, EUCENTRIC )
Temperature78 Kelvin ( 78 Kelvin - 78 Kelvin )
Camera
DetectorGatan 4kx4k
Image Acquisition
Number of Digital Images250
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwareEMAN2 SPARX
CTF Correctionwhole micrograph
Resolution By Author15
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections33478
DetailsImage processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Download
Data from EMDB
Header (meta data in XML format)emd-1994.xml (7.8 KB)
Map dataemd_1994.map.gz (421.4 KB)
Imagesem1994.png (218.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1994
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.6 KB