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RNA polymerase I initially transcribing complex with visible tandem Winged Helix domain

by single particle reconstruction, at 6.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.05, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.05, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5n61, Surface level: 0.05, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3594
TitleRNA polymerase I initially transcribing complex with visible tandem Winged Helix domain
SampleRNA polymerase I initially transcribing complex
AuthorsEngel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P
DateDeposition: 2017-02-14, Header release: 2017-03-22, Map release: 2017-04-12, Last update: 2017-09-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.05, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.05, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5n61, Surface level: 0.05, Imaged by UCSF CHIMERA

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

PDB-5n61

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleCell, Vol. 169, Issue 1, Page 120-131.e22, Year 2017
TitleStructural Basis of RNA Polymerase I Transcription Initiation.
AuthorsChristoph Engel, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, Patrick Cramer
Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, Multiprotein Complexes (chemistry), Promoter Regions, Genetic, RNA Polymerase I (chemistry, 2.7.7.6), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Transcription Initiation, Genetic, Transcription, Genetic
LinksPubMed: 28340337, PII: S0092-8674(17)30251-9, DOI: 10.1016/j.cell.2017.03.003
Map
Fileemd_3594.map.gz ( map file in CCP4 format, 143749 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
330 pix
1.13 A/pix
= 372.9 A
330 pix
1.13 A/pix
= 372.9 A
330 pix
1.13 A/pix
= 372.9 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum: -0.050090574 - 0.13193528
Average (Standard dev.): 0.0006353547 (0.008975409)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions330330330
Origin000
Limit329329329
Spacing330330330
Unit CellA= B= C: 372.9 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.13 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.131.131.13
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z372.900372.900372.900
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0500.1320.001
Supplement
Images
Images
Sample
NameRNA polymerase I initially transcribing complex
Number of Components5
Component #1: protein - RNA polymerase I initially transcribing complex
Scientific nameRNA polymerase I initially transcribing complex
Recombinant expressionNo
Component #2: protein - RNA polymerase I
Scientific nameRNA polymerase I
Theoretical Mass0.59 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae

NCBI taxonomy4932
Recombinant expressionNo
Component #3: protein - Initiation factor Rrn3
Scientific nameInitiation factor Rrn3
Theoretical Mass0.07 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae
NCBI taxonomy4932
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #4: protein - Core Factor
Scientific nameCore Factor
Theoretical Mass0.22 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae
NCBI taxonomy4932
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #5: protein - Initial transcription DNA/RNA scaffold
Scientific nameInitial transcription DNA/RNA scaffold
Theoretical Mass0.06 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae
NCBI taxonomy4932
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 32630
Expression system: synthetic construct
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 7.8
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose60 e/A**2
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorFEI FALCON II (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author6.9 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Number of Projections345000
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-3594-v19.xml (7.3 KB)
emd-3594-v20.xml (14.4 KB)
emd-3594.xml (7.3 KB)
Map dataemd_3594.map.gz (125.8 MB)
Imagesemd_3594.png (321.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3594
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 27 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, 27 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 6.2 MB
Session file for UCSF-Chimera, 4.9 MB