Modomics - A Database of RNA Modifications

ID Card:

Full name: 12S rRNA N4-methylcytidine (m4C) methyltransferase
Synonym: METT5D1
GI: 160012249
UniProt: A6NJ78
Structures: | 7PNX | 7PNY | 7PNZ |
Alpha Fold Predicted Structure: AF-A6NJ78-F1
Enzyme type: methyltransferase


PDB Structures:


7PNX

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1 ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex 2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.

Download RCSB-PDB Structures:

Pdb Files   7PNX.pdb  
Pdbx/mmCIF Files   7PNY.cif   7PNZ.cif  


Protein sequence:

MLRYPYFCRMYKECLSCWLESGIPNLGVWPNRIHTTAEKYREYEAREQTDQTQAQELHRSQDRDFETMAKLHIPVMVDEVVHCLSPQKGQIFLDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHLSELYPKQIRAMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPERGFSLRKDGPLDMRMDGGRYPDMPTAADVVNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYTRKDLLQRSTHIATKTFQALRIFVNNELNELYTGLKTAQKFLRPGGRLVALSFHSLEDRIVKRFLLGISMTERFNLSVRQQVMKTSQLGSDHENTEEVSMRRAPLMWELIHKKVLSPQDQDVQDNPRGRSAKLRAAIKL

Comments:

METTL15 methyltransferase generates m4C839 in human 12S mtrRNA





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M L R Y P Y F C R M Y K E C L S C W L E S G I P N L G V W P N R I H T T A E K Y R E Y E A R E Q T D Q T Q A Q E L H R S Q D R D F E T M A K L H I P V M V D E V V H C L S P Q K G Q I F L D M T F G S G G H T K A I L Q K E S D I V L Y A L D R D P T A Y A L A E H L S E L Y P K Q I R A M L G Q F S Q A E A L L M K A G V Q P G T F D G V L M D L G C S S M Q L D T P E R G F S L R K D G P L D M R M D G G R Y P D M P T A A D V V N A L D Q Q A L A S I L R T Y G E E K H A K K I A S A I V Q A R S I Y P I T R T Q Q L A S I V A G A F P P S A I Y T R K D L L Q R S T H I A T K T F Q A L R I F V N N E L N E L Y T G L K T A Q K F L R P G G R L V A L S F H S L E D R I V K R F L L G I S M T E R F N L S V R Q Q V M K T S Q L G S D H E N T E E V S M R R A P L M W E L I H K K V L S P Q D Q D V Q D N P R G R S A K L R A A I K L

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-A6NJ78-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-A6NJ78-F1.cif  
DSSP Secondary Structures   A6NJ78.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
METTL15 interacts with the assembly intermediate of murine mitochondrial small ribosomal subunit to form m4C840 12S rRNA residue. Ivan Laptev,Ekaterina Shvetsova,Sergey Levitskii,Marina Serebryakova,Maria Rubtsova,Victor Zgoda,Alexey Bogdanov,Piotr Kamenski,Petr Sergiev,Olga Dontsova Nucleic Acids Res [details] 32573735 -