[English] 日本語
Yorodumi
- PDB-5u0p: Cryo-EM structure of the transcriptional Mediator -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5u0p
TitleCryo-EM structure of the transcriptional Mediator
Components(Mediator complex subunit ...Mediator (coactivator)) x 16
KeywordsTRANSCRIPTION / transcription / transcriptional / Mediator / Head / Middle / Tail / Srb / RNA polymerase II / Med
Function/homologyMediator complex, subunit Med27 / Mediator complex subunit 27 / Mediator complex, subunit Med14 / Mediator complex, subunit Med31 / Mediator complex subunit MED14 / Mediator complex, subunit Med21 / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med6, fungi / MED7 protein ...Mediator complex, subunit Med27 / Mediator complex subunit 27 / Mediator complex, subunit Med14 / Mediator complex, subunit Med31 / Mediator complex subunit MED14 / Mediator complex, subunit Med21 / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med6, fungi / MED7 protein / Mediator complex, subunit Med17 / SOH1 / Mediator complex, subunit Med6 / Subunit 21 of Mediator complex / Mediator complex, subunit Med20 / Mediator complex, subunit Med8, fungi / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med18 / RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly / Subunit 17 of Mediator complex / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / MED6 mediator sub complex component / chromosome, centromeric outer repeat region / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / chromatin silencing at centromere outer repeat region / core mediator complex / Med18 protein / mediator complex / RNA polymerase II transcriptional preinitiation complex assembly / RNA polymerase II transcription cofactor activity / termination of RNA polymerase II transcription / cellular protein localization / activation of protein kinase activity / transcription by RNA polymerase II / transcription coactivator activity / regulation of transcription by RNA polymerase II / transcription, DNA-templated / nucleus / cytosol / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 22 / Uncharacterized protein C24C9.04 / Mediator of RNA polymerase II transcription subunit 31
Function and homology information
Specimen sourceSchizosaccharomyces pombe / / yeast /
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle) / Transmission electron microscopy
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.
CitationJournal: Nature / Year: 2017
Title: Mediator structure and rearrangements required for holoenzyme formation.
Authors: 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
Abstract: The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is ...The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
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

-
Components

+
Mediator complex subunit ... , 16 types, 16 molecules NFHQRTKVDGU3I2SJ

#1: Protein/peptide Mediator complex subunit 14 / Mediator (coactivator)


Mass: 105382.461 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q9P7Y4
#2: Protein/peptide Mediator complex subunit 6 / Mediator (coactivator)


Mass: 24928.947 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q9US45
#3: Protein/peptide Mediator complex subunit 8 / Mediator (coactivator)


Mass: 23360.068 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:O94646
#4: Protein/peptide Mediator complex subunit 17 / Mediator (coactivator)


Mass: 62551.410 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:P87306
#5: Protein/peptide Mediator complex subunit 18 / Mediator (coactivator)


Mass: 24056.377 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:O14198
#6: Protein/peptide Mediator complex subunit 20 / Mediator (coactivator)


Mass: 22374.775 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q10317
#7: Protein/peptide Mediator complex subunit 11 / Mediator (coactivator)


Mass: 13118.800 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q9P6Q0
#8: Protein/peptide Mediator complex subunit 22 / Mediator (coactivator)


Mass: 15396.165 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:O14010
#9: Protein/peptide Mediator complex subunit 4 / Mediator (coactivator)


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


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


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


Mass: 16913.975 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q9USH1
#13: Protein/peptide Mediator complex subunit 9 / Mediator (coactivator)


Mass: 13810.964 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:O13964
#14: Protein/peptide Mediator complex subunit 27 / Mediator (coactivator)


Mass: 31132.693 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe / References: UniProt:Q10477
#15: Protein/peptide Mediator complex subunit 19 / Mediator (coactivator)


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


Mass: 11251.861 Da / Num. of mol.: 1 / Source: (natural) Schizosaccharomyces pombe

-
Experimental details

-
Experiment

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

-
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

-
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

-
Processing

EM software
IDNameVersionCategory
1APPIONPARTICLE SELECTION
2LEGINON3.0IMAGE ACQUISITION
4CTFFIND3CTF CORRECTION
10RELION1.4INITIAL EULER ASSIGNMENT
11RELION1.4FINAL EULER ASSIGNMENT
13RELION1.4RECONSTRUCTION
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more