Modomics - A Database of RNA Modifications

ID Card:

Full name: Archaeal nucleolar protein homolog
Synonym: Nop5, AF_2088
GI: 11499670
COG: COG1498
UniProt: O28191
Structures: | 1NT2 |
Alpha Fold Predicted Structure: AF-O28191-F1
Complex: C/D RNP


PDB Structures:


1NT2

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 A resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin-Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.

Download RCSB-PDB Structures:

Pdb Files   1NT2.pdb  
Pdbx/mmCIF Files   1NT2.cif  


Protein sequence:

MSKLRYNLWFGVYDGKEIKLSENFEESFLKAENPSPLPFNVSEVGAKALGKDYYRILRKTALAVSEKMVEKELRREDRYVVALVKALEEIDESINMLNEKLEDIRAVKESEITEKFEKKIRELRELRRDVEREIEEVMEKIAPNMTELVGAKVAAKLLERAGSMERLVRLPASKIQVIGAEKSLYKAFARMKKGKKAKIPKHGIIFLHPFIRTLPKAKRGKMARFLAAKLAIAAKIDYFRGEIDESLYESIRRRYEELRRK

Comments:

Nop56/58 protein 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.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S K L R Y N L W F G V Y D G K E I K L S E N F E E S F L K A E N P S P L P F N V S E V G A K A L G K D Y Y R I L R K T A L A V S E K M V E K E L R R E D R Y V V A L V K A L E E I D E S I N M L N E K L E D I R A V K E S E I T E K F E K K I R E L R E L R R D V E R E I E E V M E K I A P N M T E L V G A K V A A K L L E R A G S M E R L V R L P A S K I Q V I G A E K S L Y K A F A R M K K G K K A K I P K H G I I F L H P F I R T L P K A K R G K M A R F L A A K L A I A A K I D Y F R G E I D E S L Y E S I R R R Y E E L R R 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-O28191-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O28191-F1.cif  
DSSP Secondary Structures   O28191.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structure and function of archaeal box C/D sRNP core proteins. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H Nat Struct Biol [details] 12598892 -