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- PDB-9pcr: Tail of Mediator of PIC-Med-SWI/SNF -

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Basic information

Entry
Database: PDB / ID: 9pcr
TitleTail of Mediator of PIC-Med-SWI/SNF
Components(Mediator of RNA polymerase II transcription subunit ...) x 6
KeywordsTRANSCRIPTION / SWI/SNF / PIC
Function / homology
Function and homology information


TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / response to endoplasmic reticulum stress / positive regulation of transcription elongation by RNA polymerase II / transcription by RNA polymerase II / transcription coregulator activity / cellular response to heat / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med15, fungi / Mediator complex, subunit Med5, fungi / Gal11, coactivator domain / Mediator complex subunit 15 / Mediator complex subunit Med5 / Gal11 activator-binding domain (ABD1) ...Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med15, fungi / Mediator complex, subunit Med5, fungi / Gal11, coactivator domain / Mediator complex subunit 15 / Mediator complex subunit Med5 / Gal11 activator-binding domain (ABD1) / Mediator complex subunit 15, KIX domain / KIX domain / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / : / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Coactivator CBP, KIX domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 3 / Mediator of RNA polymerase II transcription subunit 5 / Mediator of RNA polymerase II transcription subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYang, C. / Nagai, S. / Chen, D.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of Tail of Mediator of PIC-Med-SWI/SNF
Authors: Yang, C. / Nagai, S. / Chen, D.-H.
History
DepositionJun 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Mediator of RNA polymerase II transcription subunit 2
2: Mediator of RNA polymerase II transcription subunit 3
3: Mediator of RNA polymerase II transcription subunit 5
4: Mediator of RNA polymerase II transcription subunit 14
5: Mediator of RNA polymerase II transcription subunit 15
6: Mediator of RNA polymerase II transcription subunit 16


Theoretical massNumber of molelcules
Total (without water)575,1456
Polymers575,1456
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mediator of RNA polymerase II transcription subunit ... , 6 types, 6 molecules 123456

#1: Protein Mediator of RNA polymerase II transcription subunit 2 / Mediator complex subunit 2


Mass: 47754.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12124
#2: Protein Mediator of RNA polymerase II transcription subunit 3 / Hyper-recombination suppressor protein 1 / Mediator complex subunit 3 / Poly-glutamine domain protein 1


Mass: 43116.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40356
#3: Protein Mediator of RNA polymerase II transcription subunit 5 / Mediator complex subunit 5 / Negative regulator of URS2 protein 1


Mass: 128918.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53114
#4: Protein Mediator of RNA polymerase II transcription subunit 14 / Glucose repression regulatory protein 1 / Mediator complex subunit 14


Mass: 123500.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P19263
#5: Protein Mediator of RNA polymerase II transcription subunit 15 / Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective ...Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective silencing suppressor protein 4 / Mediator complex subunit 15 / Transcription regulatory protein GAL11 / Ty insertion suppressor protein 13


Mass: 120432.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P19659
#6: Protein Mediator of RNA polymerase II transcription subunit 16 / Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / ...Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / SWI4 suppressor protein 5 / Transcriptional silencing factor 3 / YGP1 expression regulatory protein 1


Mass: 111423.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32259

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tail of Mediator of PIC-Med-SWI/SNF / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Details: 40 mM Hepes-KOH pH 7.5, 100 mM potassium acetate, 2 mM magnesium acetate and 5 mM DTT
SpecimenEmbedding 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.20.1_4487:model refinement
3SerialEMimage acquisition
5CTFFINDCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13RELION53D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 678521 / Symmetry type: POINT

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