7OEK | pdb_00007oek

Crystal structure of the human METTL3-METTL14 complex with compound UOZ091

• PDB DOI: https://doi.org/10.2210/pdb7OEK/pdb

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


• Deposited: 2021-05-03 Released: 2021-10-20 
• Deposition Author(s): Bedi, R.K., Huang, D., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Design of Inhibitors of the m6A-RNA Writer Enzyme METTL3

Bedi, R.K., Huang, D., Li, Y., Caflisch, A.

(2023) ACS Bio Med Chem Au 

• DOI: https://doi.org/10.1021/acsbiomedchemau.3c00023

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 62.41 kDa 
• Atom Count: 3,816 
• Modeled Residue Count: 440 
• 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
VAQ (Subject of Investigation/LOI)	C [auth A]	4-[[(3S)-3-cyclopropyl-2-azaspiro[3.3]heptan-2-yl]methyl]-2-oxidanyl-N-[[(3R)-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide C34 H42 N6 O3 SVGIQPUADMIIMK-AFPLUKJUSA-N
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.9	α = 90
b = 63.9	β = 90
c = 225.49	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: 2021-10-20 
Deposition Author(s): Bedi, R.K., Huang, D., Caflisch, A.

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

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2023-06-21
  Changes: Database references, Refinement description
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary