Crystal structure of TFB1M and h45 with SAM in homo sapiens

Experimental Data Snapshot

  • Resolution: 2.99 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.

Liu, X.Shen, S.Wu, P.Li, F.Liu, X.Wang, C.Gong, Q.Wu, J.Yao, X.Zhang, H.Shi, Y.

(2019) Nucleic Acids Res 47: 7648-7665

  • DOI: https://doi.org/10.1093/nar/gkz505
  • Primary Citation of Related Structures:  
    6AAS, 6AAU, 6AAX, 6AJK

  • PubMed Abstract: 

    Mitochondria are essential molecular machinery for the maintenance of cellular energy supply by the oxidative phosphorylation system (OXPHOS). Mitochondrial transcription factor B1 (TFB1M) is a dimethyltransferase that maintains mitochondrial homeostasis by catalyzing dimethylation of two adjacent adenines located in helix45 (h45) of 12S rRNA. This m62A modification is indispensable for the assembly and maturation of human mitochondrial ribosomes. However, both the mechanism of TFB1M catalysis and the precise function of TFB1M in mitochondrial homeostasis are unknown. Here we report the crystal structures of a ternary complex of human (hs) TFB1M-h45-S-adenosyl-methionine and a binary complex hsTFB1M-h45. The structures revealed a distinct mode of hsTFB1M interaction with its rRNA substrate and with the initial enzymatic state involved in m62A modification. The suppression of hsTFB1M protein level or the overexpression of inactive hsTFB1M mutants resulted in decreased ATP production and reduced expression of components of the mitochondrial OXPHOS without affecting transcription of the corresponding genes and their localization to the mitochondria. Therefore, hsTFB1M regulated the translation of mitochondrial genes rather than their transcription via m62A modification in h45.

  • Organizational Affiliation

    School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferase 1, mitochondrial
A, C
319Homo sapiensMutation(s): 0 
Gene Names: TFB1MCGI-75
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVM0 (Homo sapiens)
Explore Q8WVM0 
Go to UniProtKB:  Q8WVM0
GTEx:  ENSG00000029639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WVM0
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (28-mer)
B, D
28Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.99 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.12α = 90
b = 104.12β = 90
c = 449.378γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31330018
Chinese Academy of SciencesChinaXDPB10, XDB08010101

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description