8BN8 | pdb_00008bn8

METTL3-METTL14 heterodimer bound to the SAM competitive small molecule inhibitor STM3006


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.193 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity.

Guirguis, A.A.Ofir-Rosenfeld, Y.Knezevic, K.Blackaby, W.Hardick, D.Chan, Y.C.Motazedian, A.Gillespie, A.Vassiliadis, D.Lam, E.Y.N.Tran, K.Andrews, B.Harbour, M.E.Vasiliauskaite, L.Saunders, C.J.Tsagkogeorga, G.Azevedo, A.Obacz, J.Pilka, E.S.Carkill, M.MacPherson, L.Wainwright, E.N.Liddicoat, B.Blyth, B.J.Albertella, M.R.Rausch, O.Dawson, M.A.

(2023) Cancer Discov 13: 2228-2247

  • DOI: https://doi.org/10.1158/2159-8290.CD-23-0007
  • Primary Citation Related Structures: 
    8BN8

  • PubMed Abstract: 

    Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic. This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.


  • Organizational Affiliation
    • Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 59.21 kDa 
  • Atom Count: 3,735 
  • Modeled Residue Count: 441 
  • Deposited Residue Count: 509 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase catalytic subunitA [auth AAA]218Homo sapiensMutation(s): 0 
Gene Names: METTL3MTA70
EC: 2.1.1.348
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase non-catalytic subunitB [auth BBB]291Homo sapiensMutation(s): 0 
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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QWR
(Subject of Investigation/LOI)

Query on QWR



Download:Ideal Coordinates CCD File
C [auth AAA]2-[[4-(6-bromanyl-2~{H}-indazol-4-yl)-1,2,3-triazol-1-yl]methyl]-6-[(4,4-dimethylpiperidin-1-yl)methyl]imidazo[1,2-a]pyridine
C25 H27 Br N8
RXIOMUYKKTZDFQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.193 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.97α = 90
b = 63.97β = 90
c = 226.48γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary
  • Version 1.3: 2026-03-04
    Changes: Refinement description