7U20

Crystal structure of human METTL1 and WDR4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of regulated m 7 G tRNA modification by METTL1-WDR4.

Li, J.Wang, L.Hahn, Q.Nowak, R.P.Viennet, T.Orellana, E.A.Roy Burman, S.S.Yue, H.Hunkeler, M.Fontana, P.Wu, H.Arthanari, H.Fischer, E.S.Gregory, R.I.

(2023) Nature 613: 391-397

  • DOI: https://doi.org/10.1038/s41586-022-05566-4
  • Primary Citation of Related Structures:  
    7U20, 8CTH, 8CTI

  • PubMed Abstract: 

    Chemical modifications of RNA have key roles in many biological processes 1-3 . N 7 -methylguanosine (m 7 G) is required for integrity and stability of a large subset of tRNAs 4-7 . The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types 8-14 . Mutations in WDR4 cause human developmental phenotypes including microcephaly 15-17 . How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive 18 . Here we show,  through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.


  • Organizational Affiliation

    Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(7)-)-methyltransferase276Homo sapiensMutation(s): 0 
Gene Names: METTL1C12orf1
EC: 2.1.1.33 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBP6 (Homo sapiens)
Explore Q9UBP6 
Go to UniProtKB:  Q9UBP6
PHAROS:  Q9UBP6
GTEx:  ENSG00000037897 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBP6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4428Homo sapiensMutation(s): 0 
Gene Names: WDR4
UniProt & NIH Common Fund Data Resources
Find proteins for P57081 (Homo sapiens)
Explore P57081 
Go to UniProtKB:  P57081
PHAROS:  P57081
GTEx:  ENSG00000160193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57081
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.407α = 90
b = 194.574β = 90
c = 86.346γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R35CA232115
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA218278
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214608

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description