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- EMDB-1435: Functional architecture of RNA polymerase I. -

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Basic information

Entry
Database: EMDB / ID: EMD-1435
TitleFunctional architecture of RNA polymerase I.
Map dataThis is the final reconstruction of RNA polymerase I in ccp4 format.
Sample
  • Sample: S. cerevisiae RNA polymerase I
  • Protein or peptide: RNA polymerase I
Function / homologyRNA polymerase I complex
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 11.9 Å
AuthorsKuhn C-D / Geiger SR / Baumli S / Gartmann M / Gerber J / Jennebach S / Mielke T / Tschochner H / Beckmann R / Cramer P
CitationJournal: Cell / Year: 2007
Title: Functional architecture of RNA polymerase I.
Authors: Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer /
Abstract: Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron ...Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming.
History
DepositionSep 27, 2007-
Header (metadata) releaseSep 27, 2007-
Map releaseJan 8, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1435.gif

Downloads & links

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Map

FileDownload / File: emd_1435.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the final reconstruction of RNA polymerase I in ccp4 format.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.23 Å/pix.
x 120 pix.
= 147.6 Å		1.23 Å/pix.
x 120 pix.
= 147.6 Å		1.23 Å/pix.
x 120 pix.
= 147.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.512 / Movie #1: 0.22
Minimum - Maximum-1.60931 - 3.05404
Average (Standard dev.)0.0329902 (±0.252014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-60-60-59
Dimensions120120120
Spacing120120120
CellA=B=C: 147.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S213
start NC/NR/NS-60-60-59
NC/NR/NS120120120
D min/max/mean-1.6093.0540.033

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Supplemental data

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Sample components

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Entire : S. cerevisiae RNA polymerase I

EntireName: S. cerevisiae RNA polymerase I
Components
  • Sample: S. cerevisiae RNA polymerase I
  • Protein or peptide: RNA polymerase I

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Supramolecule #1000: S. cerevisiae RNA polymerase I

SupramoleculeName: S. cerevisiae RNA polymerase I / type: sample / ID: 1000 / Oligomeric state: monomeric / Number unique components: 1
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa

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Macromolecule #1: RNA polymerase I

MacromoleculeName: RNA polymerase I / type: protein_or_peptide / ID: 1 / Name.synonym: DNA-dependant RNA polymerase I / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: GPY2 / synonym: Budding yeast / Cell: Yeast / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pAS22
SequenceGO: RNA polymerase I complex

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Details: 60mM ammonium sulfate, 5mM HEPES pH 7.8, 1mM magnesium chloride, 0.1mM zinc chloride
StainingType: NEGATIVE / Details: Vitrification
GridDetails: Carbon holey grids
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 100 K
DateMar 20, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Average electron dose: 20 e/Å2 / Details: Heidelberg Drum Scanner / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsQuantifoil
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 46056

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Atomic model buiding 1

Initial modelPDB ID:

1wcm

DetailsProtocol: rigid body. 1WCM (lacking Rpb4/7 and the foot domain) was fitted by manual docking using program O.
RefinementProtocol: RIGID BODY FIT

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