7RX7 | pdb_00007rx7

Structure of METTL3-METTL14(R298P) mutant methyltransferase complex

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2021-08-21 Released: 2022-11-09 
  • Deposition Author(s): Wang, P., Nam, Y.
  • Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14.

Zhang, C.Scott, R.L.Tunes, L.Hsieh, M.H.Wang, P.Kumar, A.Khadgi, B.B.Yang, Y.Y.Doxtader Lacy, K.A.Herrell, E.Zhang, X.Evers, B.Wang, Y.Xing, C.Zhu, H.Nam, Y.

(2024) Sci Adv 10: eads4750-eads4750

  • DOI: https://doi.org/10.1126/sciadv.ads4750
  • Primary Citation of Related Structures:  
    7RX6, 7RX7, 7RX8

  • PubMed Abstract: 

    Chemical modification of RNAs is important for posttranscriptional gene regulation. The METTL3-METTL14 complex generates most N 6 -methyladenosine (m 6 A) modifications in messenger RNAs (mRNAs), and dysregulated methyltransferase expression has been linked to cancers. Here we show that a changed sequence context for m 6 A can promote oncogenesis. A gain-of-function missense mutation from patients with cancer, METTL14 R298P , increases malignant cell growth in culture and transgenic mice without increasing global m 6 A levels in mRNAs. The mutant methyltransferase preferentially modifies noncanonical sites containing a GGAU motif, in vitro and in vivo. The m 6 A in GGAU context is detected by the YTH family of readers similarly to the canonical sites but is demethylated less efficiently by an eraser, ALKBH5. Combining the biochemical and structural data, we provide a model for how the cognate RNA sequences are selected for methylation by METTL3-METTL14. Our work highlights that sequence-specific m 6 A deposition is important and that increased GGAU methylation can promote oncogenesis.


  • Organizational Affiliation
    • Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase 70 kDa subunit225Homo sapiensMutation(s): 0 
Gene Names: METTL3MTA70
EC: 2.1.1.62 (PDB Primary Data), 2.1.1.348 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U44 (Homo sapiens)
Explore Q86U44 
Go to UniProtKB:  Q86U44
PHAROS:  Q86U44
GTEx:  ENSG00000165819 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86U44
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase non-catalytic subunit349Homo sapiensMutation(s): 1 
Gene Names: METTL14KIAA1627
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE5 (Homo sapiens)
Explore Q9HCE5 
Go to UniProtKB:  Q9HCE5
PHAROS:  Q9HCE5
GTEx:  ENSG00000145388 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCE5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.391α = 90
b = 101.391β = 90
c = 117.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-01-14
    Changes: Database references, Structure summary