Modomics - A Database of RNA Modifications

ID Card:

Full name: Archaeal nucleolar protein homolog
Synonym: Nop5, PF0060
GI: 18976432
COG: COG1498
UniProt: Q8U4M1
Structures: | 2NNW | 3NMU | 3NVI | 3NVK | 3NVM | 4BY9 |
Alpha Fold Predicted Structure: AF-Q8U4M1-F1
Complex: C/D RNP


PDB Structures:


2NNW

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.

Download RCSB-PDB Structures:

Pdb Files   2NNW.pdb   3NMU.pdb   3NVI.pdb   3NVK.pdb   3NVM.pdb   4BY9.pdb  
Pdbx/mmCIF Files   2NNW.cif   3NMU.cif   3NVI.cif   3NVK.cif   3NVM.cif   4BY9.cif  


Protein sequence:

MKAFISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIREIKEKYPKPPKRKREERKGKKPWKKDKKKKKKKEKPRRR

Comments:

Fused Nop56/58 protein (also designated Nop5), together with L7Ae, makes the core of C/D RNP complex in Archaea. It is a homologue of S. cerevisiae and mammalian Nop56 and Nop58 proteins (not fused). Interactions between this protein and RNA may play a role in substrate binding and/or release.





Alpha Fold Predicted Structure:






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Protein sequence:

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

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-Q8U4M1-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8U4M1-F1.cif  
DSSP Secondary Structures   Q8U4M1.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs. Oruganti S, Zhang Y, Li H, Robinson H, Terns MP, Terns RM, Yang W, Li H J Mol Biol [details] 17617422 -
Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H Mol Cell [details] 20864039 -
A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation. Ghalei H, Hsiao HH, Urlaub H, Wahl MC, Watkins NJ RNA [details] 20962039 -

Links:

_PubMed_
_Wikipedia - Small nucleolar RNA_