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- PDB-9pbi: Extra Med5/16 of PIC-Med-SWI/SNF -

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Basic information

Entry
Database: PDB / ID: 9pbi
TitleExtra Med5/16 of PIC-Med-SWI/SNF
Components
  • Mediator of RNA polymerase II transcription subunit 16
  • Mediator of RNA polymerase II transcription subunit 5
KeywordsTRANSCRIPTION / SWI/SNF / PIC
Function / homology
Function and homology information


regulation of establishment of protein localization to chromosome / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / 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 ...regulation of establishment of protein localization to chromosome / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / 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
Similarity search - Function
Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 Extra Med5/16 of PIC-Med-SWI/SNF
Authors: Yang, C. / Nagai, S. / Chen, D.-H.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 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
3: Mediator of RNA polymerase II transcription subunit 5
6: Mediator of RNA polymerase II transcription subunit 16


Theoretical massNumber of molelcules
Total (without water)240,3422
Polymers240,3422
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

#1: 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
#2: 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
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: Extra Med5/16 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 / Phase plate: OTHER

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.20.1_4487model refinement
3SerialEMimage acquisition
13RELION53D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67550 / Details: 3D auto-refine in Relion / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01513915
ELECTRON MICROSCOPYf_angle_d1.68118863
ELECTRON MICROSCOPYf_dihedral_angle_d6.4571798
ELECTRON MICROSCOPYf_chiral_restr0.0682163
ELECTRON MICROSCOPYf_plane_restr0.0132385

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