7O0M

Crystal structure of the human METTL3-METTL14 complex bound to Compound 9 (ADO_AD_023)

• PDB DOI: https://doi.org/10.2210/pdb7O0M/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-03-26 Released: 2021-09-15 
• Deposition Author(s): Bedi, R.K., Dolbois, A., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.248 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Crystal structure of the human METTL3-METTL14 complex bound to Compound 9 (ADO_AD_023)

Bedi, R.K., Dolbois, A., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.38 kDa 
• Atom Count: 3,541 
• Modelled Residue Count: 436 
• Deposited Residue Count: 536 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase catalytic subunit	A	246	Homo sapiens	Mutation(s): 0  Gene Names: METTL3, MTA70 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase non-catalytic subunit	B	290	Homo sapiens	Mutation(s): 0  Gene Names: METTL14, KIAA1627
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE5 (Homo sapiens) Explore Q9HCE5  Go to UniProtKB:  Q9HCE5
PHAROS:  Q9HCE5 GTEx:  ENSG00000145388

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UXT (Subject of Investigation/LOI)	C [auth A]	4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-9-[6-[(phenylmethyl)amino]pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one C33 H43 N7 O SMOMNPRYHLVUTG-UHFFFAOYSA-N
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
UXT	BindingDB:  7O0M	IC50: min: 26, max: 26 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.248 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.07	α = 90
b = 64.07	β = 90
c = 225.08	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Bedi, R.K., Dolbois, A., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description