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- EMDB-50242: CryoEM structure of Human Mediator subunit MED23 complexed with p... -

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Basic information

Entry
Database: EMDB / ID: EMD-50242
TitleCryoEM structure of Human Mediator subunit MED23 complexed with phosphorylated Elk-1 transcription factor
Map data
Sample
  • Complex: Complex between human Mediator subunit Med23 and phosphorylated transcription factor Elk1
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 23
    • Protein or peptide: Green fluorescent protein,ETS domain-containing protein Elk-1
KeywordsMediator complex / transcription factor / Med23 / ELK-1 / phosphorylation / GENE REGULATION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsMonte D / Verger A / Lens Z / villeret V
Funding support France, 1 items
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, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50242.png

Downloads & links

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Map

FileDownload / File: emd_50242.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302. Å		1.18 Å/pix.
x 256 pix.
= 302. Å		1.18 Å/pix.
x 256 pix.
= 302. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17969 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.06851073 - 1.6775997
Average (Standard dev.)0.0006723461 (±0.022902297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50242_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50242_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex between human Mediator subunit Med23 and phosphorylated t...

EntireName: Complex between human Mediator subunit Med23 and phosphorylated transcription factor Elk1
Components
  • Complex: Complex between human Mediator subunit Med23 and phosphorylated transcription factor Elk1
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 23
    • Protein or peptide: Green fluorescent protein,ETS domain-containing protein Elk-1

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Supramolecule #1: Complex between human Mediator subunit Med23 and phosphorylated t...

SupramoleculeName: Complex between human Mediator subunit Med23 and phosphorylated transcription factor Elk1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mediator of RNA polymerase II transcription subunit 23

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 23
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 158.294891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: METQLQSIFE EVVKTEVIEE AFPGMFMDTP EDEKTKLISC LGAFRQFWGG LSQESHEQCI QWIVKFIHGQ HSPKRISFLY DCLAMAVET GLLPPRLVCE SLINSDTLEW ERTQLWALTF KLVRKIIGGV DYKGVRDLLK VILEKILTIP NTVSSAVVQQ L LAAREVIA ...String:
METQLQSIFE EVVKTEVIEE AFPGMFMDTP EDEKTKLISC LGAFRQFWGG LSQESHEQCI QWIVKFIHGQ HSPKRISFLY DCLAMAVET GLLPPRLVCE SLINSDTLEW ERTQLWALTF KLVRKIIGGV DYKGVRDLLK VILEKILTIP NTVSSAVVQQ L LAAREVIA YILERNACLL PAYFAVTEIR KLYPEGKLPH WLLGNLVSDF VDTFRPTARI NSICGRCSLL PVVNNSGAIC NS WKLDPAT LRFPLKGLLP YDKDLFEPQT ALLRYVLEQP YSRDMVCNML GLNKQHKQRC PVLEDQLVDL VVYAMERSET EEK FDDGGT SQLLWQHLSS QLIFFVLFQF ASFPHMVLSL HQKLAGRGLI KGRDHLMWVL LQFISGSIQK NALADFLPVM KLFD LLYPE KEYIPVPDIN KPQSTHAFAM TCIWIHLNRK AQNDNSKLQI PIPHSLRLHH EFLQQSLRNK SLQMNDYKIA LLCNA YSTN SECFTLPMGA LVETIYGNGI MRIPLPGTNC MASGSITPLP MNLLDSLTVH AKMSLIHSIA TRVIKLAHAK SSVALA PAL VETYSRLLVY MEIESLGIKG FISQLLPTVF KSHAWGILHT LLEMFSYRMH HIQPHYRVQL LSHLHTLAAV AQTNQNQ LH LCVESTALRL ITALGSSEVQ PQFTRFLSDP KTVLSAESEE LNRALILTLA RATHVTDFFT GSDSIQGTWC KDILQTIM S FTPHNWASHT LSCFPGPLQA FFKQNNVPQE SRFNLKKNVE EEYRKWKSMS NENDIITHFS MQGSPPLFLC LLWKMLLET DHINQIGYRV LERIGARALV AHVRTFADFL VYEFSTSAGG QQLNKCIEIL NDMVWKYNIV TLDRLILCLA MRSHEGNEAQ VCYFIIQLL LLKPNDFRNR VSDFVKENSP EHWLQNDWHT KHMNYHKKYP EKLYFEGLAE QVDPPVQIQS PYLPIYFGNV C LRFLPVFD IVIHRFLELL PVSKSLETLL DHLGGLYKFH DRPVTYLYNT LHYYEMHLRD RAFLKRKLVH AIIGSLKDNR PQ GWCLSDT YLKCAMNARE ENPWVPDDTY YCRLIGRLVD TMAGKSPGPF PNCDWRFNEF PNPAAHALHV TCVELMALAV SGK EVGNAL LNVVLKSQPL VPRENITAWM NAIGLIITAL PEPYWIVLHD RIVSVISSPS LTSETEWVGY PFRLFDFTAC HQSY SEMSC SYTLALAHAV WHHSSIGQLS LIPKFLTEVL LPIVKTEFQL LYVYHLVGPF LQRFQQERTR CMIEIGVAFY DMLLN VDQC STHLNYMDPI CDFLYHMKYM FTGDSVKEQV EKIICNLKPA LKLRLRFITH ISKMEPAAVP PQAMNSGSPA PQSNQV PVS LPVTQDVLFQ GPGHHHHHH

UniProtKB: Mediator of RNA polymerase II transcription subunit 23

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Macromolecule #2: Green fluorescent protein,ETS domain-containing protein Elk-1

MacromoleculeName: Green fluorescent protein,ETS domain-containing protein Elk-1
type: protein_or_peptide / ID: 2
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
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.627406 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK N GIKVNFKI ...String:
MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK N GIKVNFKI RHNIEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KG SSQPQKG RKPRDLELPL SPSLLGGPGP ERAPGSGSGS GLQAPGPALA PSLLPTHTLA PVLLTPSSLP PSIHFWSTL (SEP)PIAPRSPAK LSFQFPSSGH HHHHH

UniProtKB: Green fluorescent protein, ETS domain-containing protein Elk-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6h02

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 346324
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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