6FDL | pdb_00006fdl

Crystal structure of the NYN domain of human MARF1

• PDB DOI: https://doi.org/10.2210/pdb6FDL/pdb

• 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 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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

• PubMed: 30364987 
• DOI: https://doi.org/10.1093/nar/gky1011
• Primary Citation 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.
Department of Biochemistry, University of Zurich, Switzerland.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Department of Oncology, McGill University, Montreal, Quebec, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.47 kDa 
• Atom Count: 2,528 
• Modeled Residue Count: 301 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiosis regulator and mRNA stability factor 1	A, B	160	Homo sapiens	Mutation(s): 2  Gene Names: MARF1, KIAA0430, LKAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4F3 (Homo sapiens) Explore Q9Y4F3  Go to UniProtKB:  Q9Y4F3
PHAROS:  Q9Y4F3 GTEx:  ENSG00000166783

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.867	α = 90
b = 96.867	β = 90
c = 63.096	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Jinek, M., Brandmann, T.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research	Canada	MOP-130425
Canadian Institutes of Health Research	Canada	FDN143301
Natural Sciences and Engineering Research Council (Canada)	Canada	RGPIN-2015-03712
Natural Sciences and Engineering Research Council (Canada)	Canada	RGPIN-2014-06434
European Research Council	Switzerland	ERC-StG-337284

Revision History  

• 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