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- PDB-9f76: CryoEM structure of human Mediator subunit Med23 -

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Basic information

Entry
Database: PDB / ID: 9f76
TitleCryoEM structure of human Mediator subunit Med23
ComponentsMediator of RNA polymerase II transcription subunit 23
KeywordsTRANSCRIPTION / Mediator / MED23 / human
Function / homology
Function and homology information


positive regulation of T cell extravasation / core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression ...positive regulation of T cell extravasation / core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / transcription coactivator activity / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex, subunit Med23 / Mediator complex subunit 23
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMonte, D. / Verger, A. / Lens, Z. / Villeret, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE12-0021 France
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of human Mediator recruitment by the phosphorylated transcription factor Elk-1.
Authors: Didier Monté / Zoé Lens / Frédérique Dewitte / Marcus Fislage / Marc Aumercier / Alexis Verger / Vincent Villeret /
Abstract: One function of Mediator complex subunit MED23 is to mediate transcriptional activation by the phosphorylated transcription factor Elk-1, in response to the Ras-MAPK signaling pathway. Using ...One function of Mediator complex subunit MED23 is to mediate transcriptional activation by the phosphorylated transcription factor Elk-1, in response to the Ras-MAPK signaling pathway. Using cryogenic electron microscopy, we solve a 3.0 Å structure of human MED23 complexed with the phosphorylated activation domain of Elk-1. Elk-1 binds to MED23 via a hydrophobic sequence PSIHFWSTLSP containing one phosphorylated residue (S383), which forms a tight turn around the central Phenylalanine. Binding of Elk-1 induces allosteric changes in MED23 that propagate to the opposite face of the subunit, resulting in the dynamic behavior of a 19-residue segment, which alters the molecular surface of MED23. We design a specific MED23 mutation (G382F) that disrupts Elk--1 binding and consequently impairs Elk-1-dependent serum-induced activation of target genes in the Ras-Raf-MEK-ERK signaling pathway. The structure provides molecular details and insights into a Mediator subunit-transcription factor interface.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 23


Theoretical massNumber of molelcules
Total (without water)158,2951
Polymers158,2951
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 23 / Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator complex subunit 23 / Protein sur-2 homolog / hSur-2 / Transcriptional coactivator CRSP130 / Vitamin D3 receptor-interacting protein complex 130 kDa component / DRIP130


Mass: 158294.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Med23 sequence with C-terminal His Tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MED23, ARC130, CRSP3, DRIP130, KIAA1216, SUR2 / Cell (production host): ExpiSF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULK4
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: Human Mediator subunit Med23 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: ExpiSF9
Buffer solutionpH: 7.5 / Details: 20mM Tris/HCl, 100mM NaCl, 1mM TCEP
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K / Details: blotting time 5.6sec, blot force 2

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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 defocus max: 1700 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
13PHENIX3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2559224
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95624 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6H03

6h03


Pdb chain-ID: A / Accession code: 6H03 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210447
ELECTRON MICROSCOPYf_angle_d0.52814199
ELECTRON MICROSCOPYf_dihedral_angle_d3.5471358
ELECTRON MICROSCOPYf_chiral_restr0.0381608
ELECTRON MICROSCOPYf_plane_restr0.0061784

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