6AKJ

The crystal structure of EMC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing.

Xie, G.Vo, T.V.Thillainadesan, G.Holla, S.Zhang, B.Jiang, Y.Lv, M.Xu, Z.Wang, C.Balachandran, V.Shi, Y.Li, F.Grewal, S.I.S.

(2019) Nat Commun 10: 251-251

  • DOI: https://doi.org/10.1038/s41467-018-08273-9
  • Primary Citation of Related Structures:  
    6AKJ

  • PubMed Abstract: 

    Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1 Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1∆ due to termination defects are revealed in mmi1 W112A . Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enhancer of rudimentary homolog,YTH domain-containing protein mmi1 fusion protein
A, B
155Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O74958 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74958 
Go to UniProtKB:  O74958
Find proteins for G2TRN4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore G2TRN4 
Go to UniProtKB:  G2TRN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO74958G2TRN4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.689α = 90
b = 86.689β = 90
c = 105.391γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2019-02-13 
  • Deposition Author(s): Li, F.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description