6FDL

Crystal structure of the NYN domain of human MARF1

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2017-12-26 Released: 2018-11-07 
  • Deposition Author(s): Jinek, M., Brandmann, T.
  • Funding Organization(s): Canadian Institutes of Health Research, Natural Sciences and Engineering Research Council (Canada), European Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs.

Nishimura, T.Fakim, H.Brandmann, T.Youn, J.Y.Gingras, A.C.Jinek, M.Fabian, M.R.

(2018) Nucleic Acids Res 46: 12008-12021

  • DOI: https://doi.org/10.1093/nar/gky1011
  • Primary Citation of Related Structures:  
    6FDL

  • PubMed Abstract: 

    Meiosis arrest female 1 (MARF1) is a cytoplasmic RNA binding protein that is essential for meiotic progression of mouse oocytes, in part by limiting retrotransposon expression. MARF1 is also expressed in somatic cells and tissues; however, its mechanism of action has yet to be investigated. Human MARF1 contains a NYN-like domain, two RRMs and eight LOTUS domains. Here we provide evidence that MARF1 post-transcriptionally silences targeted mRNAs. MARF1 physically interacts with the DCP1:DCP2 mRNA decapping complex but not with deadenylation machineries. Importantly, we provide a 1.7 Å resolution crystal structure of the human MARF1 NYN domain, which we demonstrate is a bona fide endoribonuclease, the activity of which is essential for the repression of MARF1-targeted mRNAs. Thus, MARF1 post-transcriptionally represses gene expression by serving as both an endoribonuclease and as a platform that recruits the DCP1:DCP2 decapping complex to targeted mRNAs.


  • Organizational Affiliation

    Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis regulator and mRNA stability factor 1
A, B
160Homo sapiensMutation(s): 2 
Gene Names: MARF1KIAA0430LKAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4F3 (Homo sapiens)
Explore Q9Y4F3 
Go to UniProtKB:  Q9Y4F3
PHAROS:  Q9Y4F3
GTEx:  ENSG00000166783 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4F3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.867α = 90
b = 96.867β = 90
c = 63.096γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-130425
Canadian Institutes of Health ResearchCanadaFDN143301
Natural Sciences and Engineering Research Council (Canada)CanadaRGPIN-2015-03712
Natural Sciences and Engineering Research Council (Canada)CanadaRGPIN-2014-06434
European Research CouncilSwitzerlandERC-StG-337284

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary