6AJK

Crystal structure of TFB1M and h45 in homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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

    Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dimethyladenosine transferase 1, mitochondrialA320Homo 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
PHAROS:  Q8WVM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WVM0
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (28-MER)B28Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.564α = 90
b = 122.564β = 90
c = 73.067γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31330018,31870760
Chinese Academy of SciencesChinaXDPB10
Chinese Academy of SciencesChinaXDB08010101

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