8D58

Crystal structure of human METTL1-WDR4 complex

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2022-06-04 Released: 2023-01-11 
  • Deposition Author(s): Raj, R., Babu, K., Nam, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures and mechanisms of tRNA methylation by METTL1-WDR4.

Ruiz-Arroyo, V.M.Raj, R.Babu, K.Onolbaatar, O.Roberts, P.H.Nam, Y.

(2023) Nature 613: 383-390

  • DOI: https://doi.org/10.1038/s41586-022-05565-5
  • Primary Citation of Related Structures:  
    8D58, 8D59, 8D5B, 8D9K, 8D9L, 8EG0

  • PubMed Abstract: 

    Specific, regulated modification of RNAs is important for proper gene expression 1,2 . tRNAs are rich with various chemical modifications that affect their stability and function 3,4 . 7-Methylguanosine (m 7 G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth 5,6 . The METTL1-WDR4 complex generates m 7 G46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers 7-22 . Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1-WDR4 and cryo-electron microscopy structures of METTL1-WDR4-tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1-WDR4-tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m 7 G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m 7 G modification by METTL1, providing the framework to understand its contribution to biology and disease.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(7)-)-methyltransferase246Homo sapiensMutation(s): 0 
Gene Names: METTL1C12orf1
EC: 2.1.1.33 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBP6 (Homo sapiens)
Explore Q9UBP6 
Go to UniProtKB:  Q9UBP6
PHAROS:  Q9UBP6
GTEx:  ENSG00000037897 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBP6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4405Homo sapiensMutation(s): 0 
Gene Names: WDR4
UniProt & NIH Common Fund Data Resources
Find proteins for P57081 (Homo sapiens)
Explore P57081 
Go to UniProtKB:  P57081
PHAROS:  P57081
GTEx:  ENSG00000160193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57081
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
G [auth B]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.495α = 90
b = 91.113β = 90
c = 122.83γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM122960
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP190259
Welch FoundationUnited StatesI-2115-20220331

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description