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- PDB-9f6y: CryoEM structure of Human Mediator subunit MED23 complexed with p... -

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Basic information

Entry
Database: PDB / ID: 9f6y
TitleCryoEM structure of Human Mediator subunit MED23 complexed with phosphorylated Elk-1 transcription factor
Components
  • Green fluorescent protein,ETS domain-containing protein Elk-1
  • Mediator of RNA polymerase II transcription subunit 23
KeywordsGENE REGULATION / Mediator complex / transcription factor / Med23 / ELK-1 / phosphorylation
Function / homology
Function and homology information


positive regulation of T cell extravasation / hippocampal neuron apoptotic process / response to fibroblast growth factor / core mediator complex / mediator complex binding / cellular response to testosterone stimulus / NGF-stimulated transcription / mediator complex / transcription regulator activator activity / Generic Transcription Pathway ...positive regulation of T cell extravasation / hippocampal neuron apoptotic process / response to fibroblast growth factor / core mediator complex / mediator complex binding / cellular response to testosterone stimulus / NGF-stimulated transcription / mediator complex / transcription regulator activator activity / Generic Transcription Pathway / RSV-host interactions / ERK/MAPK targets / response to light stimulus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of transcription initiation by RNA polymerase II / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / axon terminus / bioluminescence / liver development / generation of precursor metabolites and energy / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / lung development / mitochondrial membrane / PPARA activates gene expression / cellular response to gamma radiation / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / sequence-specific double-stranded DNA binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / neuronal cell body / dendrite / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex, subunit Med23 / Mediator complex subunit 23 / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Green fluorescent protein, GFP ...Mediator complex, subunit Med23 / Mediator complex subunit 23 / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ETS domain-containing protein Elk-1 / Green fluorescent protein / Mediator of RNA polymerase II transcription subunit 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 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 2, 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

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 23
B: Green fluorescent protein,ETS domain-containing protein Elk-1


Theoretical massNumber of molelcules
Total (without water)195,9222
Polymers195,9222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area53350 Å2
MethodPISA

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: MED23, ARC130, CRSP3, DRIP130, KIAA1216, SUR2 / Cell line (production host): ExpiSF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULK4
#2: Protein Green fluorescent protein,ETS domain-containing protein Elk-1


Mass: 37627.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fusion between GFP and ELK-1 transactivation domain (308-401) mutated at positions T336, T333, T353 and T363 (mutated to Ala) + C-terminal his tag,fusion between GFP and ELK-1 ...Details: fusion between GFP and ELK-1 transactivation domain (308-401) mutated at positions T336, T333, T353 and T363 (mutated to Ala) + C-terminal his tag,fusion between GFP and ELK-1 transactivation domain (308-401) mutated at positions T336, T333, T353 and T363 (mutated to Ala) + C-terminal his tag,fusion between GFP and ELK-1 transactivation domain (308-401) mutated at positions T336, T333, T353 and T363 (mutated to Ala) + C-terminal his tag,fusion between GFP and ELK-1 transactivation domain (308-401) mutated at positions T336, T333, T353 and T363 (mutated to Ala) + C-terminal his tag
Source: (gene. exp.) Homo sapiens (human) / Gene: GFP, ELK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212, UniProt: P19419
Has ligand of interestY
Has protein modificationY

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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: Complex between human Mediator subunit Med23 and phosphorylated transcription factor Elk1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
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: 63.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346324 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002510336
ELECTRON MICROSCOPYf_angle_d0.573614052
ELECTRON MICROSCOPYf_chiral_restr0.04021589
ELECTRON MICROSCOPYf_plane_restr0.00511762
ELECTRON MICROSCOPYf_dihedral_angle_d4.11381341

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