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- EMDB-4148: Free monomeric RNA polymerase I at 4.0A resolution -

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Basic information

Entry
Database: EMDB / ID: 4148
TitleFree monomeric RNA polymerase I at 4.0A resolution
SampleYeast RNA polymerase I elongation complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map dataSharpened map (B=-149A^2)
Methodsingle particle reconstruction, at 4 A resolution
AuthorsNeyer S / Kunz M
CitationNature, 2016

Nature, 2016 StrPapers
Structure of RNA polymerase I transcribing ribosomal DNA genes.
Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis

DateDeposition: Oct 15, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Nov 23, 2016 / Last update: Oct 15, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5m3m
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_4148.map.gz (map file in CCP4 format, 48669 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
230 pix
1.05 A/pix
= 241.5 A
230 pix
1.05 A/pix
= 241.5 A
230 pix
1.05 A/pix
= 241.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 A
Density
Contour Level:0.04 (by author), 0.03 (movie #1):
Minimum - Maximum-0.09353096 - 0.15214713
Average (Standard dev.)-3.5655336E-5 (0.0072155506)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions230230230
Origin000
Limit229229229
Spacing230230230
CellA=B=C: 241.49998 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.051.051.05
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z241.500241.500241.500
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0940.152-0.000

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Supplemental data

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Sample components

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Entire Yeast RNA polymerase I elongation complex

EntireName: Yeast RNA polymerase I elongation complex / Number of components: 17
MassTheoretical: 590 kDa

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Component #1: protein, Yeast RNA polymerase I elongation complex

ProteinName: Yeast RNA polymerase I elongation complex / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #2: protein, DNA-directed RNA polymerase I subunit RPA190

ProteinName: DNA-directed RNA polymerase I subunit RPA190 / Recombinant expression: No
MassTheoretical: 186.676969 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #3: protein, DNA-directed RNA polymerase I subunit RPA135

ProteinName: DNA-directed RNA polymerase I subunit RPA135 / Recombinant expression: No
MassTheoretical: 135.910328 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #4: protein, DNA-directed RNA polymerases I and III subunit RPAC1

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1 / Recombinant expression: No
MassTheoretical: 37.732613 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #5: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #8: protein, DNA-directed RNA polymerase I subunit RPA12

ProteinName: DNA-directed RNA polymerase I subunit RPA12 / Recombinant expression: No
MassTheoretical: 13.676566 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #10: protein, DNA-directed RNA polymerases I and III subunit RPAC2

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC2 / Recombinant expression: No
MassTheoretical: 16.16786 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #12: protein, DNA-directed RNA polymerase I subunit RPA49

ProteinName: DNA-directed RNA polymerase I subunit RPA49 / Recombinant expression: No
MassTheoretical: 46.721707 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #13: protein, DNA-directed RNA polymerase I subunit RPA34

ProteinName: DNA-directed RNA polymerase I subunit RPA34 / Recombinant expression: No
MassTheoretical: 26.933518 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #14: protein, DNA-directed RNA polymerase I subunit RPA14

ProteinName: DNA-directed RNA polymerase I subunit RPA14 / Recombinant expression: No
MassTheoretical: 14.599128 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #15: protein, DNA-directed RNA polymerase I subunit RPA43

ProteinName: DNA-directed RNA polymerase I subunit RPA43 / Recombinant expression: No
MassTheoretical: 36.264852 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #16: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #17: ligand, SULFATE ION

LigandName: SULFATE ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.606305 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: blot force 13, blotting time 8.5s

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 56 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 94000
3D reconstructionSoftware: Relion / Resolution: 4 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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