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- PDB-5u0s: Cryo-EM structure of the Mediator-RNAPII complex -

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Entry
Database: PDB / ID: 5u0s
TitleCryo-EM structure of the Mediator-RNAPII complex
DescriptorMediator of RNA polymerase II transcription subunit 6
Mediator of RNA polymerase II transcription subunit 8
Mediator of RNA polymerase II transcription subunit 17
Mediator of RNA polymerase II transcription subunit 18
Mediator of RNA polymerase II transcription subunit 20
and more 13 items
KeywordsTRANSCRIPTION/TRANSFERASE / transcriptional / transcription / Mediator / Srb / RNA polymerase II / RNA / Pol2 / activation / complex / TRANSCRIPTION-TRANSFERASE complex
Specimen sourceSchizosaccharomyces pombe / yeast / Fission yeast / シゾサッカロミセス・ポンベ /
MethodElectron microscopy (7.8 A resolution / Single particle)
AuthorsTsai, K.-L. / Yu, X. / Gopalan, S. / Chao, T.-C. / Zhang, Y. / Florens, L. / Washburn, M.P. / Murakami, K. / Conaway, R.C. / Conaway, J.W. / Asturias, F.
CitationNature, 2017

Nature, 2017 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 / Release: Mar 8, 2017 / Last modification: Mar 15, 2017

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Assembly

Deposited unit
F: Mediator complex subunit 6
H: Mediator complex subunit 8
Q: Mediator complex subunit 17
R: Mediator complex subunit 18
T: Mediator complex subunit 20
K: Mediator complex subunit 11
V: Mediator complex subunit 22
N: Mediator complex subunit 14
D: Mediator complex subunit 4
G: Mediator complex subunit 7
U: Mediator complex subunit 21
3: Mediator complex subunit 31
2: Mediator complex subunit 27
I: Mediator complex subunit 9
S: Mediator complex subunit 19
J: Mediator complex subunit 10
a: RNA polymerase II subunit Rpb1
b: RNA polymerase II subunit Rpb2
c: RNA polymerase II subunit Rpb3
d: RNA polymerase II subunit Rpb4
e: RNA polymerase II subunit Rpb5
f: RNA polymerase II subunit Rpb6
g: RNA polymerase II subunit Rpb7
h: RNA polymerase II subunit Rpb8
i: RNA polymerase II subunit Rpb9
j: RNA polymerase II subunit Rpb10
k: RNA polymerase II subunit Rpb11
l: RNA polymerase II subunit Rpb12


Theoretical massNumber of molelcules
Total (without water)953,38228
Polyers953,38228
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polypeptide(L) , 28 types, 28 molecules FHQRTKVNDG...

#1: Polypeptide(L)Mediator complex subunit 6


Mass: 24928.947 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9US45
#2: Polypeptide(L)Mediator complex subunit 8


Mass: 23360.068 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O94646
#3: Polypeptide(L)Mediator complex subunit 17


Mass: 62551.410 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P87306
#4: Polypeptide(L)Mediator complex subunit 18


Mass: 24056.377 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O14198
#5: Polypeptide(L)Mediator complex subunit 20


Mass: 22374.775 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q10317
#6: Polypeptide(L)Mediator complex subunit 11


Mass: 13118.800 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9P6Q0
#7: Polypeptide(L)Mediator complex subunit 22


Mass: 15396.165 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O14010
#8: Polypeptide(L)Mediator complex subunit 14


Mass: 105382.461 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9P7Y4
#9: Polypeptide(L)Mediator complex subunit 4


Mass: 20358.010 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe
#10: Polypeptide(L)Mediator complex subunit 7


Mass: 43573.094 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O60104
#11: Polypeptide(L)Mediator complex subunit 21


Mass: 15821.031 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O94376
#12: Polypeptide(L)Mediator complex subunit 31


Mass: 16913.975 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9USH1
#13: Polypeptide(L)Mediator complex subunit 27


Mass: 31132.693 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q10477
#14: Polypeptide(L)Mediator complex subunit 9


Mass: 13810.964 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O13964
#15: Polypeptide(L)Mediator complex subunit 19


Mass: 11847.596 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe
#16: Polypeptide(L)Mediator complex subunit 10


Mass: 11251.861 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe
#17: Polypeptide(L)RNA polymerase II subunit Rpb1


Mass: 194372.625 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P36594, EC: 2.7.7.6
#18: Polypeptide(L)RNA polymerase II subunit Rpb2


Mass: 138027.188 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q02061, EC: 2.7.7.6
#19: Polypeptide(L)RNA polymerase II subunit Rpb3


Mass: 33748.816 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P37382
#20: Polypeptide(L)RNA polymerase II subunit Rpb4


Mass: 15379.490 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O74825
#21: Polypeptide(L)RNA polymerase II subunit Rpb5


Mass: 23954.504 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q09191
#22: Polypeptide(L)RNA polymerase II subunit Rpb6


Mass: 15742.497 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P36595
#23: Polypeptide(L)RNA polymerase II subunit Rpb7


Mass: 19121.982 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O14459
#24: Polypeptide(L)RNA polymerase II subunit Rpb8


Mass: 14317.318 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q92399
#25: Polypeptide(L)RNA polymerase II subunit Rpb9


Mass: 13192.771 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O74635
#26: Polypeptide(L)RNA polymerase II subunit Rpb10


Mass: 8286.801 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O13877
#27: Polypeptide(L)RNA polymerase II subunit Rpb11


Mass: 14143.276 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P87123
#28: Polypeptide(L)RNA polymerase II subunit Rpb12


Mass: 7216.495 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P48011

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: complex of Mediator and RNAPII / Type: COMPLEX
Buffer solutionDetails: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: C-Flat CF-2/2-4C
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Processing

3D reconstructionResolution: 7.8 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 3862

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