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- EMDB-3959: Apo RNA Polymerase III -

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Basic information

Entry
Database: EMDB / ID: EMD-3959
TitleApo RNA Polymerase III
Map dataApo RNA Polymerase III
Sample
  • Complex: Apo RNA Polymerase III
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAbascal-Palacios G / Ramsay EP / Beuron F / Morris E / Vannini A
CitationJournal: Nature / Year: 2018
Title: Structural basis of RNA polymerase III transcription initiation.
Authors: Guillermo Abascal-Palacios / Ewan Phillip Ramsay / Fabienne Beuron / Edward Morris / Alessandro Vannini /
Abstract: RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. ...RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.
History
DepositionOct 27, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseJan 31, 2018-
UpdateJan 31, 2018-
Current statusJan 31, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3959.png

Downloads & links

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Map

FileDownload / File: emd_3959.map.gz / Format: CCP4 / Size: 111.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo RNA Polymerase III
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 308 pix.
= 162.008 Å		0.53 Å/pix.
x 308 pix.
= 162.008 Å		0.53 Å/pix.
x 308 pix.
= 162.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.5260.5260.526
CCP4 map header0.5260.5260.526
EM Navigator Movie #11.051.051.05
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.28058112 - 0.5130126
Average (Standard dev.)0.0006352922 (±0.009676342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions308308308
Spacing308308308
CellA=B=C: 162.00801 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5260.5260.526
M x/y/z308308308
origin x/y/z0.0000.0000.000
length x/y/z162.008162.008162.008
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS308308308
D min/max/mean-0.2810.5130.001

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Supplemental data

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Sample components

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Entire : Apo RNA Polymerase III

EntireName: Apo RNA Polymerase III
Components
  • Complex: Apo RNA Polymerase III

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Supramolecule #1: Apo RNA Polymerase III

SupramoleculeName: Apo RNA Polymerase III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.5)
Startup modelType of model: EMDB MAP
EMDB ID:

3179

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.2) / Number images used: 62306
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.2)
FSC plot (resolution estimation)

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