6S2W | pdb_00006s2w

Structure of S. pombe Erh1, a protein important for meiotic mRNA decay in mitosis and meiosis progression.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6S2W

This is version 1.1 of the entry. See complete history

Literature

Formation of S. pombe Erh1 homodimer mediates gametogenic gene silencing and meiosis progression.

Hazra, D.Andric, V.Palancade, B.Rougemaille, M.Graille, M.

(2020) Sci Rep 10: 1034-1034

  • DOI: https://doi.org/10.1038/s41598-020-57872-4
  • Primary Citation Related Structures: 
    6S2W

  • PubMed Abstract: 

    Timely and accurate expression of the genetic information relies on the integration of environmental cues and the activation of regulatory networks involving transcriptional and post-transcriptional mechanisms. In fission yeast, meiosis-specific transcripts are selectively targeted for degradation during mitosis by the EMC complex, composed of Erh1, the ortholog of human ERH, and the YTH family RNA-binding protein Mmi1. Here, we present the crystal structure of Erh1 and show that it assembles as a homodimer. Mutations of amino acid residues to disrupt Erh1 homodimer formation result in loss-of-function phenotypes, similar to erh1∆ cells: expression of meiotic genes is derepressed in mitotic cells and meiosis progression is severely compromised. Interestingly, formation of Erh1 homodimer is dispensable for interaction with Mmi1, suggesting that only fully assembled EMC complexes consisting of two Mmi1 molecules bridged by an Erh1 dimer are functionally competent. We also show that Erh1 does not contribute to Mmi1-dependent down-regulation of the meiosis regulator Mei2, supporting the notion that Mmi1 performs additional functions beyond EMC. Overall, our results provide a structural basis for the assembly of the EMC complex and highlight its biological relevance in gametogenic gene silencing and meiosis progression.


  • Organizational Affiliation
    • BIOC, CNRS, Ecole Polytechnique, IP Paris, F-91128, Palaiseau, France.

Macromolecule Content 

  • Total Structure Weight: 38.48 kDa 
  • Atom Count: 2,417 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 327 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enhancer of rudimentary-like protein
A, B, C
109Schizosaccharomyces pombeMutation(s): 0 
Gene Names: Erh1
UniProt
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 GroupG2TRN4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
H [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth B],
F [auth B],
G [auth B],
J [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY

Query on ACY



Download:Ideal Coordinates CCD File
I [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.845α = 90
b = 123.847β = 90
c = 68.144γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description