9F76 | pdb_00009f76

CryoEM structure of human Mediator subunit Med23


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9F76

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 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.

Macromolecule Content 

  • Total Structure Weight: 158.29 kDa 
  • Atom Count: 10,179 
  • Modeled Residue Count: 1,258 
  • Deposited Residue Count: 1,382 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONPHENIX

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