8IPM

The structure of human mitochondrial methyltransferase METTL15 with h44_RNA, RBFA and SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15.

Lv, M.Zhou, W.Hao, Y.Li, F.Zhang, H.Yao, X.Shi, Y.Zhang, L.

(2024) Cell Discov 10: 11-11

  • DOI: https://doi.org/10.1038/s41421-023-00634-z
  • Primary Citation of Related Structures:  
    8IPI, 8IPK, 8IPL, 8IPM

  • PubMed Abstract: 

    Mitochondrial rRNA modifications are essential for mitoribosome assembly and its proper function. The m 4 C methyltransferase METTL15 maintains mitochondrial homeostasis by catalyzing m 4 C839 located in 12 S rRNA helix 44 (h44). This modification is essential to fine-tuning the ribosomal decoding center and increasing decoding fidelity according to studies of a conserved site in Escherichia coli. Here, we reported a series of crystal structures of human METTL15-hsRBFA-h44-SAM analog, METTL15-hsRBFA-SAM, METTL15-SAM and apo METTL15. The structures presented specific interactions of METTL15 with different substrates and revealed that hsRBFA recruits METTL15 to mitochondrial small subunit for further modification instead of 12 S rRNA. Finally, we found that METTL15 deficiency caused increased reactive oxygen species, decreased membrane potential and altered cellular metabolic state. Knocking down METTL15 caused an elevated lactate secretion and increased levels of histone H4K12-lactylation and H3K9-lactylation. METTL15 might be a suitable model to study the regulation between mitochondrial metabolism and histone lactylation.


  • Organizational Affiliation

    Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. lmq123@ustc.edu.cn.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome-binding factor A, mitochondrialA [auth C]34Homo sapiensMutation(s): 0 
Gene Names: RBFAC18orf22
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N0V3 (Homo sapiens)
Explore Q8N0V3 
Go to UniProtKB:  Q8N0V3
PHAROS:  Q8N0V3
GTEx:  ENSG00000101546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N0V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
12S rRNA N4-methylcytidine (m4C) methyltransferaseB [auth D]338Homo sapiensMutation(s): 0 
Gene Names: METTL15METT5D1
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for A6NJ78 (Homo sapiens)
Explore A6NJ78 
Go to UniProtKB:  A6NJ78
PHAROS:  A6NJ78
GTEx:  ENSG00000169519 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NJ78
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*GP*AP*CP*CP*GP*CP*CP*CP*GP*UP*AP*AP*CP*GP*GP*UP*CP*G)-3')C [auth A]19Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFG (Subject of Investigation/LOI)
Query on SFG

Download Ideal Coordinates CCD File 
D
SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.22α = 90
b = 134.111β = 90
c = 93.026γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32293213, 32100958, 32090042 and 31870760

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references