Modomics - A Database of RNA Modifications

ID Card:

Full name: Nucleolar protein 2
Synonym: Yna1, N2428, YNL2428W
GI: 730166
Orf: YNL061W
COG: COG0144
UniProt: P40991
Structures: | 6ELZ | 6EM5 |
Alpha Fold Predicted Structure: AF-P40991-F1
Enzyme type: methyltransferase
Position of modification - modification: l:2870(2501) - m5C


PDB Structures:


6ELZ

Structure Description:

Title: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosmes
Classification: RIBOSOME
Technique: Electron Microscopy
Resolution: 3.30
Aggregation State: PARTICLE
Reconstruction method: SINGLE PARTICLE

Abstract of the PDB Structure's related Publication:

Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.

Download RCSB-PDB Structures:

Pdb Files   6EM5.pdb  
Pdbx/mmCIF Files   6ELZ.cif   6EM5.cif  


Protein sequence:

MGSRRHKNKQAAPPTLEEFQARKEKKANRKLEKGKRPSTTQGDEVSDRKKKKSKPFKKSRKEEEEVVEEDKDLPEVDLEELSKARKSLFDDEEDDDEAGLVDEELKDEFDLEQEYDYDEDEDNDAHPIFSDDDDEADLEELNAQNMEALSKKLDEEEAEEAEEAEMELVEAENMQPRADILPTEEQEEMMAQETPNLTSTRTRMIEIVKVLENFKTLGAEGRSRGEYVDRLLKDICEYFGYTPFLAEKLFNLFSPAEAMEFFEANEIARPITIRTNTLKTRRRDLAQTLVNRGVNLQPIGSWTKVGLQIFDSQVPIGATPEYLAGHYILQAASSFLPVIALDPHENERILDMAAAPGGKTTYISAMMKNTGCVFANDANKSRTKSLIANIHRLGCTNTIVCNYDAREFPKVIGGFDRILLDAPCSGTGVIGKDQSVKVSRTEKDFIQIPHLQKQLLLSAIDSVDCNSKHGGVIVYSTCSVAVEEDEAVIDYALRKRPNVKLVDTGLAIGKEAFTSYRGKKFHPSVKLARRYYPHTYNVDGFFVAKFQKIGPSSFDDNQASAKEKETAARKEALEEGIIHSDFATFEDEEDDKYIEKSVKNNLLKKGVNPKAKRPSNEK

Comments:

The nucleolar Nop2 protein binds 27S pre-rRNA. Loss of m5C2870 affects ribosome synthesis and processing.





Alpha Fold Predicted Structure:




Parsing response... [524026/561442]


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Protein sequence:

M G S R R H K N K Q A A P P T L E E F Q A R K E K K A N R K L E K G K R P S T T Q G D E V S D R K K K K S K P F K K S R K E E E E V V E E D K D L P E V D L E E L S K A R K S L F D D E E D D D E A G L V D E E L K D E F D L E Q E Y D Y D E D E D N D A H P I F S D D D D E A D L E E L N A Q N M E A L S K K L D E E E A E E A E E A E M E L V E A E N M Q P R A D I L P T E E Q E E M M A Q E T P N L T S T R T R M I E I V K V L E N F K T L G A E G R S R G E Y V D R L L K D I C E Y F G Y T P F L A E K L F N L F S P A E A M E F F E A N E I A R P I T I R T N T L K T R R R D L A Q T L V N R G V N L Q P I G S W T K V G L Q I F D S Q V P I G A T P E Y L A G H Y I L Q A A S S F L P V I A L D P H E N E R I L D M A A A P G G K T T Y I S A M M K N T G C V F A N D A N K S R T K S L I A N I H R L G C T N T I V C N Y D A R E F P K V I G G F D R I L L D A P C S G T G V I G K D Q S V K V S R T E K D F I Q I P H L Q K Q L L L S A I D S V D C N S K H G G V I V Y S T C S V A V E E D E A V I D Y A L R K R P N V K L V D T G L A I G K E A F T S Y R G K K F H P S V K L A R R Y Y P H T Y N V D G F F V A K F Q K I G P S S F D D N Q A S A K E K E T A A R K E A L E E G I I H S D F A T F E D E E D D K Y I E K S V K N N L L K K G V N P K A K R P S N E K
50100150200250300350400450500550600SequenceGHTBSN

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-P40991-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P40991-F1.cif  
DSSP Secondary Structures   P40991.dssp  





Publications: