9F6Y | pdb_00009f6y

CryoEM structure of Human Mediator subunit MED23 complexed with phosphorylated Elk-1 transcription factor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of human Mediator recruitment by the phosphorylated transcription factor Elk-1.

Monte, D.Lens, Z.Dewitte, F.Fislage, M.Aumercier, M.Verger, A.Villeret, V.

(2025) Nat Commun 16: 3772-3772

  • DOI: https://doi.org/10.1038/s41467-025-59014-8
  • Primary Citation of Related Structures:  
    9F6Y, 9F76

  • PubMed 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 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 PSIHFWSTLS P P containing one phosphorylated residue (S383 p ), 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.


  • Organizational Affiliation
    • CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France. Didier.Monte@univ-lille.fr.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 231,382Homo sapiensMutation(s): 0 
Gene Names: MED23ARC130CRSP3DRIP130KIAA1216SUR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULK4 (Homo sapiens)
Explore Q9ULK4 
Go to UniProtKB:  Q9ULK4
PHAROS:  Q9ULK4
GTEx:  ENSG00000112282 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULK4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,ETS domain-containing protein Elk-1341Homo sapiensMutation(s): 3 
Gene Names: GFPELK1
UniProt & NIH Common Fund Data Resources
Find proteins for P19419 (Homo sapiens)
Explore P19419 
Go to UniProtKB:  P19419
PHAROS:  P19419
GTEx:  ENSG00000126767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19419
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-16-CE12-0021

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release