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YEAST RNA POLYMERASE III

by single particle reconstruction, at 21 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0035, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0035, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1753
TitleYEAST RNA POLYMERASE III
MapRNA-Polymerase III in its free form
SampleRNA polymerase III
KeywordsTranscription, RNA polymerase, tRNA
AuthorsVannini A, Ringel R, Kusser AG, Berninghausen O, Kassavetis GA, Cramer P
DateDeposition: 2010-06-30, Header release: 2010-07-23, Map release: 2010-10-08, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0035, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0035, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell, Vol. 143, Issue 1, Page 59-70, Year 2010
TitleMolecular basis of RNA polymerase III transcription repression by Maf1.
AuthorsAlessandro Vannini, Rieke Ringel, Anselm G Kusser, Otto Berninghausen, George A Kassavetis, Patrick Cramer
Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
KeywordsAmino Acid Sequence, MAF1 protein, S cerevisiae, Molecular Sequence Data, Multiprotein Complexes (chemistry), Promoter Regions, Genetic, RNA Polymerase III (antagonists & inhibitors, 2.7.7.-), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Sequence Alignment, Transcription Factors (chemistry), Transcription, Genetic
LinksPII: S0092-8674(10)01012-3, DOI: 10.1016/j.cell.2010.09.002, PubMed: 20887893
Map
Fileemd_1753.map.gz ( map file in CCP4 format, 2849 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
3.31 A/pix
= 297.9 A
90 pix
3.31 A/pix
= 297.9 A
90 pix
3.31 A/pix
= 297.9 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0035 (by author), 0.0035 (movie #1):
Minimum - Maximum: -0.00569051 - 0.253301
Average (Standard dev.): 0.00280515 (0.0138798)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin000
Limit898989
Spacing909090
Unit CellA= B= C: 297.9 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.31 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.313.313.31
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z297.900297.900297.900
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0060.2530.003
Annotation DetailsRNA-Polymerase III in its free form
Supplement
Images
Images
Sample
NameRNA polymerase III
Number of Components1
Oligomeric StateMonomeric
Theoretical Mass0.7MDa
DetailsThe sample was monodisperse
Mass-estimation MethodNative Mass Spectrometry
Experimental Mass0.7MDa
Component #1: protein - RNA polymerase III
Scientific nameRNA polymerase III
Theoretical Mass0.7 MDa
Experimental Mass0.7 MDa
Oligomeric DetailsMonomeric
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's Yeast
NCBI taxonomy4932
StrainNZ-16
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Engineered SourceNCBI taxonomy: 4932
Expression system: Saccharomyces cerevisiae
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
Specimen Support DetailsQuantifoil R3/3 2nm carbon pre-coated holey grids
Specimen Stateparticle
BufferDetails: 20mM Hepes pH 7.8, 50 mM Ammonium Sulfate, 0.1 mM MgCl2, 0.01 mM ZnCl2, 5mM DTT
pH: 7.8
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot, FEI
Humidity95
InstrumentFEI VITROBOT
Temperature184 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeOTHER
Lens
Imaging ModeOTHER
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Camera
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author21 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections20480
Download
Data from EMDB
Header (meta data in XML format)emd-1753.xml (6.5 KB)
Map dataemd_1753.map.gz (2.7 MB)
Images1753.tif (1.5 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1753
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.3 KB