6GT5

METTL16 MTase domain (crystal form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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. Electronic address: ramesh.pillai@unige.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferaseA, B291Homo sapiensMutation(s): 0 
Gene Names: METTL16METT10D
EC: 2.1.1.346 (PDB Primary Data), 2.1.1.62 (PDB Primary Data), 2.1.1.348 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W50 (Homo sapiens)
Explore Q86W50 
Go to UniProtKB:  Q86W50
PHAROS:  Q86W50
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/579 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.55α = 90
b = 89.55β = 90
c = 179.13γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
AutoPROCdata scaling
STARANISOdata scaling
PHASERphasing
BUSTERrefinement
Cootmodel building

Structure Validation

View Full Validation Report




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