delta-N METTL16 MTase domain

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
A, B, C
251Homo sapiensMutation(s): 0 
Gene Names: METTL16METT10D
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W50 (Homo sapiens)
Explore Q86W50 
Go to UniProtKB:  Q86W50
GTEx:  ENSG00000127804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86W50
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.768α = 90
b = 133.768β = 90
c = 78.701γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling

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