Modomics - A Database of RNA Modifications

ID Card:

Full name: Nucleolar protein 58
Synonym: Nop5p
GI: 2833225
Orf: YOR310C
COG: COG1498
UniProt: Q12499
Structures: | 5WLC | 5WYJ | 5WYK | 6KE6 | 6LQP | 6LQQ | 6LQR | 6LQS | 6LQT | 6LQU | 6LQV | 6ND4 | 6ZQA | 6ZQB | 6ZQC | 6ZQD | 6ZQE | 7AJT | 7AJU |
Alpha Fold Predicted Structure: AF-Q12499-F1
Complex: C/D RNP


PDB Structures:


5WLC

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.

Download RCSB-PDB Structures:

Pdb Files   6ND4.pdb   7AJT.pdb  
Pdbx/mmCIF Files   5WLC.cif   5WYJ.cif   5WYK.cif   6KE6.cif   6LQP.cif   6LQQ.cif   6LQR.cif   6LQS.cif   6LQT.cif   6LQU.cif   6LQV.cif   6ND4.cif   6ZQA.cif   6ZQB.cif   6ZQC.cif   6ZQD.cif   6ZQE.cif   7AJT.cif   7AJU.cif  


Protein sequence:

MAYVLTETSAGYALLKASDKKIYKSSSLIQDLDSSDKVLKEFKIAAFSKFNSAANALEEANSIIEGKVSSQLEKLLEEIKKDKKSTLIVSETKLANAINKLGLNFNVVSDAVTLDIYRAIKEYLPELLPGMSDNDLSKMSLGLAHSIGRHKLKFSADKVDVMIIQAIALLDDLDKELNTYAMRCKEWYGWHFPELAKIVTDSVAYARIILTMGIRSKASETDLSEILPEEIEERVKTAAEVSMGTEITQTDLDNINALAEQIVEFAAYREQLSNYLSARMKAIAPNLTQLVGELVGARLIAHSGSLISLAKSPASTIQILGAEKALFRALKTKHDTPKYGLLYHASLVGQATGKNKGKIARVLAAKAAVSLRYDALAEDRDDSGDIGLESRAKVENRLSQLEGRDLRTTPKVVREAKKVEMTEARAYNADADTAKAASDSESDSDDEEEEKKEKKEKKRKRDDDEDSKDSKKAKKEKKDKKEKKEKKEKKEKKEKKEKKEKKSKKEKKEKK

Comments:

Required for pre-18S rRNA processing. May bind microtubules. Interacts with NOP56p and NOP1p. Together with Nop56 and Snu13 makes a core of the C/D RNP complex.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q12499-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q12499-F1.cif  
DSSP Secondary Structures   Q12499.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Nop5p is a small nucleolar ribonucleoprotein component required for pre-18 S rRNA processing in yeast. Wu P, Brockenbrough JS, Metcalfe AC, Chen S, Aris JP J Biol Chem [details] 9632712 -
Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Gautier T, Berges T, Tollervey D, Hurt E Mol Cell Biol [details] 9372940 -
Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing. van Nues RW, Granneman S, Kudla G, Sloan KE, Chicken M, Tollervey D, Watkins NJ EMBO J [details] 21556049 -

Links:

_SGD_
_PubMed_