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Functional architecture of RNA polymerase I.

by single particle reconstruction, at 11.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.22, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.22, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1435
AuthorsKuhn C-D, Geiger SR, Baumli S, Gartmann M, Gerber J, Jennebach S, Mielke T, Tschochner H, Beckmann R, Cramer P
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.22, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.22, Made by UCSF CHIMERA

Supplemental images

1435.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Article
Citation - Primary
ArticleCell, Vol. 131, Issue 7, Page 1260-72, Year 2007
TitleFunctional architecture of RNA polymerase I.
AuthorsClaus-D Kuhn, Sebastian R Geiger, Sonja Baumli, Marco Gartmann, Jochen Gerber, Stefan Jennebach, Thorsten Mielke, Herbert Tschochner, Roland Beckmann, Patrick Cramer
Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
KeywordsBinding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, DNA Polymerase I (chemistry, 2.7.7.-), Models, Molecular, Mutation, POL1 protein, S cerevisiae (2.7.7.7), Peptide Elongation Factors (chemistry), Peptide Initiation Factors (chemistry), Promoter Regions, Genetic, Protein Conformation, Protein Interaction Domains and Motifs, Protein Interaction Mapping, Protein Structure, Tertiary, Protein Subunits, RNA Processing, Post-Transcriptional, RNA, Ribosomal (genetics), Saccharomyces cerevisiae (enzymology), Saccharomyces cerevisiae Proteins (chemistry), Structure-Activity Relationship, Transcription Factors, TFII (chemistry), Transcription, Genetic, Transcriptional Elongation Factors (chemistry), transcription factor S-II, transcription factor TFIIF
LinksPII: S0092-8674(07)01414-6, DOI: 10.1016/j.cell.2007.10.051, PubMed: 18160037
Map
FileEMD-1435.map ( map file in CCP4 format, 6913 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (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:0.512, 0.22 (movie #1):
Minimum - Maximum: -1.60931 - 3.05404
Average (Standard dev.): 0.0329902 (0.252014)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : Y X Z
Dimensions : 120 120 120
Origin : -60 -60 -59
Limit : 59 59 60
Spacing : 120 120 120
Unit CellA = 147.6 A , B = 147.6 A , C = 147.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.23 A , Y = 1.23 A , Z = 1.23 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.231.231.23
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z147.600147.600147.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S213
start NC/NR/NS-60-60-59
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.6093.0540.033
Annotation DetailsThis is the final reconstruction of RNA polymerase I in ccp4 format.
Supplement
Images
Images

1435.gif
Sample
NameS. cerevisiae RNA polymerase I
Oligomeric Statemonomeric
Number of Components1
Experimental Mass0.6 MDa
Theoretical Mass0.6 MDa
Component #1: protein - DNA-dependant RNA polymerase I
Scientific nameRNA polymerase I
Common NameDNA-dependant RNA polymerase I
Theoretical Mass0.6 MDa
Experimental Mass0.6 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBudding yeast
StrainGPY2
Recombinant expressionYes
Natural SourceCell: Yeast
Organelle: Nucleus
Cell Location: Nucleus
Engineered SourceVector: pAS22
Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
LinksGene Ontology: GO:0005736
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
StainingVitrification
Specimen Support DetailsCarbon holey grids
Specimen Stateparticle
BufferDetails: 60mM ammonium sulfate, 5mM HEPES pH 7.8, 1mM magnesium chloride, 0.1mM zinc chloride
pH: 7.8
Vitrification
Cryogen NameETHANE
Humidity95
InstrumentFEI VITROBOT
DetailsVitrification instrument: Vitrobot
Imaging
MicroscopeFEI TECNAI F30
Date2006-03-20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeOTHER
Lens
MagnificationNominal: 39000 X,
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric ( OTHER )
Tilt Angle0 degrees - 0 degrees
Temperature100 Kelvin
Camera
DetectorKodak Film
Image Acquisition
Quant Bit Number16
ScannerPRIMESCAN
DetailsHeidelberg Drum Scanner
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwareSPIDER
Resolution By Author11.9
Resolution MethodFSC at 0.5
Single Particle
Number of Projections46056
DetailsQuantifoil
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
DetailsProtocol: rigid body. 1WCM (lacking Rpb4/7 and the foot domain) was fitted by manual docking using program O.
Download
Data from EMDB
Header (meta data in XML format)emd-1435.xml (7.6 KB)
Map dataemd_1435.map.gz (710.6 KB)
Images1435.gif (20.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1435
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.7 KB