5K7W

Crystal structure of the catalytic domain of Mettl3/Mettl14 complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases.

Wang, P.Doxtader, K.A.Nam, Y.

(2016) Mol Cell 63: 306-317

  • DOI: 10.1016/j.molcel.2016.05.041
  • Primary Citation of Related Structures:  
    5K7U, 5K7W, 5K7M

  • PubMed Abstract: 
  • N(6)-methyladenosine (m(6)A) is a prevalent, reversible chemical modification of functional RNAs and is important for central events in biology. The core m(6)A writers are Mettl3 and Mettl14, which both contain methyltransferase domains. How Mettl3 and Mettl14 cooperate to catalyze methylation of adenosines has remained elusive ...

    N(6)-methyladenosine (m(6)A) is a prevalent, reversible chemical modification of functional RNAs and is important for central events in biology. The core m(6)A writers are Mettl3 and Mettl14, which both contain methyltransferase domains. How Mettl3 and Mettl14 cooperate to catalyze methylation of adenosines has remained elusive. We present crystal structures of the complex of Mettl3/Mettl14 methyltransferase domains in apo form as well as with bound S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) in the catalytic site. We determine that the heterodimeric complex of methyltransferase domains, combined with CCCH motifs, constitutes the minimally required regions for creating m(6)A modifications in vitro. We also show that Mettl3 is the catalytically active subunit, while Mettl14 plays a structural role critical for substrate recognition. Our model provides a molecular explanation for why certain mutations of Mettl3 and Mettl14 lead to impaired function of the methyltransferase complex.


    Organizational Affiliation

    Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: yunsun.nam@utsouthwestern.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase 70 kDa subunit A225Homo sapiensMutation(s): 0 
Gene Names: METTL3MTA70
EC: 2.1.1.62 (PDB Primary Data), 2.1.1.348 (UniProt)
Find proteins for Q86U44 (Homo sapiens)
Explore Q86U44 
Go to UniProtKB:  Q86U44
NIH Common Fund Data Resources
PHAROS:  Q86U44
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase subunit METTL14 B349Homo sapiensMutation(s): 0 
Gene Names: METTL14KIAA1627
EC: 2.1.1.62
Find proteins for Q9HCE5 (Homo sapiens)
Explore Q9HCE5 
Go to UniProtKB:  Q9HCE5
NIH Common Fund Data Resources
PHAROS:  Q9HCE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/349 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.942α = 90
b = 101.942β = 90
c = 118.009γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pew ScholarUnited States--
Packard FellowUnited States--
Welch FoundationUnited StatesI-1851
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR1221

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-08-10
    Changes: Database references
  • Version 1.3: 2019-04-24
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence