6GFN

METTL16 MTase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development.

Mendel, M.Chen, K.M.Homolka, D.Gos, P.Pandey, R.R.McCarthy, A.A.Pillai, R.S.

(2018) Mol Cell 71: 986-1000.e11

  • DOI: https://doi.org/10.1016/j.molcel.2018.08.004
  • Primary Citation of Related Structures:  
    6GFK, 6GFN, 6GT5

  • PubMed Abstract: 

    Internal modification of RNAs with N 6 -methyladenosine (m 6 A) is a highly conserved means of gene expression control. While the METTL3/METTL14 heterodimer adds this mark on thousands of transcripts in a single-stranded context, the substrate requirements and physiological roles of the second m 6 A writer METTL16 remain unknown. Here we describe the crystal structure of human METTL16 to reveal a methyltransferase domain furnished with an extra N-terminal module, which together form a deep-cut groove that is essential for RNA binding. When presented with a random pool of RNAs, METTL16 selects for methylation-structured RNAs where the critical adenosine is present in a bulge. Mouse 16-cell embryos lacking Mettl16 display reduced mRNA levels of its methylation target, the SAM synthetase Mat2a. The consequence is massive transcriptome dysregulation in ∼64-cell blastocysts that are unfit for further development. This highlights the role of an m 6 A RNA methyltransferase in facilitating early development via regulation of SAM availability.


  • Organizational Affiliation

    Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase291Homo sapiensMutation(s): 0 
Gene Names: METTL16METT10D
EC: 2.1.1.346 (PDB Primary Data), 2.1.1.62 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W50 (Homo sapiens)
Explore Q86W50 
Go to UniProtKB:  Q86W50
PHAROS:  Q86W50
GTEx:  ENSG00000127804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86W50
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.36α = 90
b = 92.36β = 90
c = 180.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandGermMethylation and Origin-of-pi

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description