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- PDB-5u0p: Cryo-EM structure of the transcriptional Mediator -

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Entry
Database: PDB / ID: 5u0p
TitleCryo-EM structure of the transcriptional Mediator
Descriptor(Mediator complex subunit ...) x 16
KeywordsTRANSCRIPTION / transcription / transcriptional / Mediator / Head / Middle / Tail / Srb / RNA polymerase II / Med
Specimen sourceSchizosaccharomyces pombe / yeast / Fission yeast / シゾサッカロミセス・ポンベ /
MethodElectron microscopy (4.4 Å resolution / Particle / 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, 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 26, 2016 / Release: Mar 8, 2017
RevisionDateData content typeGroupProviderType
1.0Mar 8, 2017Structure modelrepositoryInitial release
1.1Mar 15, 2017Structure modelDatabase references
1.2Apr 19, 2017Structure modelDatabase references

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Structure visualization

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Assembly

Deposited unit
N: Mediator complex subunit 14
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
D: Mediator complex subunit 4
G: Mediator complex subunit 7
U: Mediator complex subunit 21
3: Mediator complex subunit 31
I: Mediator complex subunit 9
2: Mediator complex subunit 27
S: Mediator complex subunit 19
J: Mediator complex subunit 10


Theoretical massNumber of molelcules
Total (without water)455,87816
Polyers455,87816
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mediator complex subunit ... , 16 types, 16 molecules NFHQRTKVDG...

#1: Polypeptide(L)Mediator complex subunit 14


Mass: 105382.461 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9P7Y4

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription from RNA polymerase II promoter (GO: 0006366)
#2: Polypeptide(L)Mediator complex subunit 6


Mass: 24928.947 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9US45

Cellular component

Molecular function

  • RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly (GO: 0001128)

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • RNA polymerase II transcriptional preinitiation complex assembly (GO: 0051123)
#3: Polypeptide(L)Mediator complex subunit 8


Mass: 23360.068 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O94646

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

#4: Polypeptide(L)Mediator complex subunit 17


Mass: 62551.410 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: P87306

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription, DNA-templated (GO: 0006351)
#5: Polypeptide(L)Mediator complex subunit 18


Mass: 24056.377 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O14198

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • termination of RNA polymerase II transcription (GO: 0006369)
#6: Polypeptide(L)Mediator complex subunit 20


Mass: 22374.775 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q10317

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • cellular protein localization (GO: 0034613)
  • chromatin silencing at centromere outer repeat region (GO: 1990141)
  • transcription from RNA polymerase II promoter (GO: 0006366)
#7: Polypeptide(L)Mediator complex subunit 11


Mass: 13118.800 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9P6Q0

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • transcription from RNA polymerase II promoter (GO: 0006366)
#8: Polypeptide(L)Mediator complex subunit 22


Mass: 15396.165 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O14010

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription, DNA-templated (GO: 0006351)
#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

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

#11: Polypeptide(L)Mediator complex subunit 21


Mass: 15821.031 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O94376

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription from RNA polymerase II promoter (GO: 0006366)
#12: Polypeptide(L)Mediator complex subunit 31


Mass: 16913.975 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q9USH1

Cellular component

Molecular function

  • RNA polymerase II transcription cofactor activity (GO: 0001104)
  • transcription coactivator activity (GO: 0003713)

Biological process

  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription from RNA polymerase II promoter (GO: 0006366)
#13: Polypeptide(L)Mediator complex subunit 9


Mass: 13810.964 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: O13964

Cellular component

#14: Polypeptide(L)Mediator complex subunit 27


Mass: 31132.693 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt: Q10477

Cellular component

Biological process

  • activation of protein kinase activity (GO: 0032147)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • transcription, DNA-templated (GO: 0006351)
#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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Mediator complex / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe
Buffer solutionDetails: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40
pH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 9.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 11181

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging ID
1APPIONPARTICLE SELECTION1
2LEGINON3.0IMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
13RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42484 / Symmetry type: POINT

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