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- EMDB-8480: Cryo-EM map of the Mediator-RNAPII complex -

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Basic information

Entry
Database: EMDB / ID: 8480
TitleCryo-EM map of the Mediator-RNAPII complex
Samplecomplex of Mediator and RNAPII
SourceSchizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /
Map dataMediator-RNAPII complex
Methodsingle particle reconstruction, at 7.8 A resolution
AuthorsTsai K-L / Yu X
CitationNature, 2017, 544, 196-201

Nature, 2017, 544, 196-201 StrPapers
Mediator structure and rearrangements required for holoenzyme formation.
Kuang-Lei Tsai / Xiaodi Yu / Sneha Gopalan / Ti-Chun Chao / Ying Zhang / Laurence Florens / Michael P Washburn / Kenji Murakami / Ronald C Conaway / Joan W Conaway / Francisco J Asturias

DateDeposition: Nov 26, 2016 / Header (metadata) release: Mar 8, 2017 / Map release: Mar 8, 2017 / Last update: Nov 26, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5u0s
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Orientation
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Supplemental images

Downloads & links

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Map

Fileemd_8480.map.gz (map file in CCP4 format, 21808 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
176 pix
2.62 A/pix
= 461.12 A
176 pix
2.62 A/pix
= 461.12 A
176 pix
2.62 A/pix
= 461.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.62 A
Density
Contour Level:0.08 (by emdb), 0.08 (movie #1):
Minimum - Maximum-0.11419473 - 0.22855034
Average (Standard dev.)-0.000103825936 (0.014926006)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions176176176
Origin000
Limit175175175
Spacing176176176
CellA=B=C: 461.12 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.622.622.62
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z461.120461.120461.120
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.1140.229-0.000

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Supplemental data

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Sample components

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Entire complex of Mediator and RNAPII

EntireName: complex of Mediator and RNAPII / Number of components: 29
MassTheoretical: 1.5 MDa

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Component #1: protein, complex of Mediator and RNAPII

ProteinName: complex of Mediator and RNAPII / Recombinant expression: No
MassTheoretical: 1.5 MDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #2: protein, Mediator complex subunit 6

ProteinName: Mediator complex subunit 6 / Recombinant expression: No
MassTheoretical: 24.928947 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #3: protein, Mediator complex subunit 8

ProteinName: Mediator complex subunit 8 / Recombinant expression: No
MassTheoretical: 23.360068 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #4: protein, Mediator complex subunit 17

ProteinName: Mediator complex subunit 17 / Recombinant expression: No
MassTheoretical: 62.55141 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #5: protein, Mediator complex subunit 18

ProteinName: Mediator complex subunit 18 / Recombinant expression: No
MassTheoretical: 24.056377 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #6: protein, Mediator complex subunit 20

ProteinName: Mediator complex subunit 20 / Recombinant expression: No
MassTheoretical: 22.374775 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #7: protein, Mediator complex subunit 11

ProteinName: Mediator complex subunit 11 / Recombinant expression: No
MassTheoretical: 13.1188 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #8: protein, Mediator complex subunit 22

ProteinName: Mediator complex subunit 22 / Recombinant expression: No
MassTheoretical: 15.396165 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #9: protein, Mediator complex subunit 14

ProteinName: Mediator complex subunit 14 / Recombinant expression: No
MassTheoretical: 105.382461 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #10: protein, Mediator complex subunit 4

ProteinName: Mediator complex subunit 4 / Recombinant expression: No
MassTheoretical: 20.35801 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #11: protein, Mediator complex subunit 7

ProteinName: Mediator complex subunit 7 / Recombinant expression: No
MassTheoretical: 43.573094 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #12: protein, Mediator complex subunit 21

ProteinName: Mediator complex subunit 21 / Recombinant expression: No
MassTheoretical: 15.821031 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #13: protein, Mediator complex subunit 31

ProteinName: Mediator complex subunit 31 / Recombinant expression: No
MassTheoretical: 16.913975 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #14: protein, Mediator complex subunit 27

ProteinName: Mediator complex subunit 27 / Recombinant expression: No
MassTheoretical: 31.132693 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #15: protein, Mediator complex subunit 9

ProteinName: Mediator complex subunit 9 / Recombinant expression: No
MassTheoretical: 13.810964 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #16: protein, Mediator complex subunit 19

ProteinName: Mediator complex subunit 19 / Recombinant expression: No
MassTheoretical: 11.847596 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #17: protein, Mediator complex subunit 10

ProteinName: Mediator complex subunit 10 / Recombinant expression: No
MassTheoretical: 11.251861 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #18: protein, RNA polymerase II subunit Rpb1

ProteinName: RNA polymerase II subunit Rpb1 / Recombinant expression: No
MassTheoretical: 194.372625 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #19: protein, RNA polymerase II subunit Rpb2

ProteinName: RNA polymerase II subunit Rpb2 / Recombinant expression: No
MassTheoretical: 138.027188 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #20: protein, RNA polymerase II subunit Rpb3

ProteinName: RNA polymerase II subunit Rpb3 / Recombinant expression: No
MassTheoretical: 33.748816 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #21: protein, RNA polymerase II subunit Rpb4

ProteinName: RNA polymerase II subunit Rpb4 / Recombinant expression: No
MassTheoretical: 15.37949 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #22: protein, RNA polymerase II subunit Rpb5

ProteinName: RNA polymerase II subunit Rpb5 / Recombinant expression: No
MassTheoretical: 23.954504 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #23: protein, RNA polymerase II subunit Rpb6

ProteinName: RNA polymerase II subunit Rpb6 / Recombinant expression: No
MassTheoretical: 15.742497 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #24: protein, RNA polymerase II subunit Rpb7

ProteinName: RNA polymerase II subunit Rpb7 / Recombinant expression: No
MassTheoretical: 19.121982 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #25: protein, RNA polymerase II subunit Rpb8

ProteinName: RNA polymerase II subunit Rpb8 / Recombinant expression: No
MassTheoretical: 14.317318 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #26: protein, RNA polymerase II subunit Rpb9

ProteinName: RNA polymerase II subunit Rpb9 / Recombinant expression: No
MassTheoretical: 13.192771 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #27: protein, RNA polymerase II subunit Rpb10

ProteinName: RNA polymerase II subunit Rpb10 / Recombinant expression: No
MassTheoretical: 8.286801 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #28: protein, RNA polymerase II subunit Rpb11

ProteinName: RNA polymerase II subunit Rpb11 / Recombinant expression: No
MassTheoretical: 14.143276 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Component #29: protein, RNA polymerase II subunit Rpb12

ProteinName: RNA polymerase II subunit Rpb12 / Recombinant expression: No
MassTheoretical: 7.216495 kDa
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40
pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 9.6 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 3862
3D reconstructionSoftware: RELION / Resolution: 7.8 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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