Crystal structure of the vertebrate conserved region (VCR) of human METTL16

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

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Mechanistic insights into m6A modification of U6 snRNA by human METTL16.

Aoyama, T.Yamashita, S.Tomita, K.

(2020) Nucleic Acids Res 48: 5157-5168

  • DOI: https://doi.org/10.1093/nar/gkaa227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The N6-methyladenosine modification at position 43 (m6A43) of U6 snRNA is catalyzed by METTL16, and is important for the 5'-splice site recognition by U6 snRNA during pre-mRNA splicing. Human METTL16 consists of the N-terminal methyltransferase domain (MTD) and the C-terminal vertebrate conserved region (VCR). While the MTD has an intrinsic property to recognize a specific sequence in the distinct structural context of RNA, the VCR functions have remained uncharacterized. Here, we present structural and functional analyses of the human METTL16 VCR. The VCR increases the affinity of METTL16 toward U6 snRNA, and the conserved basic region in VCR is important for the METTL16-U6 snRNA interaction. The VCR structure is topologically homologous to the C-terminal RNA binding domain, KA1, in U6 snRNA-specific terminal uridylyl transferase 1 (TUT1). A chimera of the N-terminal MTD of METTL16 and the C-terminal KA1 of TUT1 methylated U6 snRNA more efficiently than the MTD, indicating the functional conservation of the VCR and KA1 for U6 snRNA biogenesis. The VCR interacts with the internal stem-loop (ISL) within U6 snRNA, and this interaction would induce the conformational rearrangement of the A43-containing region of U6 snRNA, thereby modifying the RNA structure to become suitable for productive catalysis by the MTD. Therefore, the MTD and VCR in METTL16 cooperatively facilitate the m6A43 U6 snRNA modification.

  • Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA N6-adenosine-methyltransferase METTL16,RNA N6-adenosine-methyltransferase METTL16164Homo 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

  • Resolution: 2.79 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.61α = 90
b = 139.61β = 90
c = 53.13γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H03980
Japan Society for the Promotion of Science (JSPS)Japan18J23142
Japan Society for the Promotion of Science (JSPS)Japan26113002

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references