Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal protein L7Ae
GI: 159111753
Orf: GL50803_11287
COG: COG1358
UniProt: A8BMJ0
Structures: | 3O85 |
Alpha Fold Predicted Structure: AF-A8BMJ0-F1
Complex: C/D RNP


PDB Structures:


3O85

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Box C/D ribonucleoproteins (RNP) guide the 2'-O-methylation of targeted nucleotides in archaeal and eukaryotic rRNAs. The archaeal L7Ae and eukaryotic 15.5kD box C/D RNP core protein homologues initiate RNP assembly by recognizing kink-turn (K-turn) motifs. The crystal structure of the 15.5kD core protein from the primitive eukaryote Giardia lamblia is described here to a resolution of 1.8 Å. The Giardia 15.5kD protein exhibits the typical α-β-α sandwich fold exhibited by both archaeal L7Ae and eukaryotic 15.5kD proteins. Characteristic of eukaryotic homologues, the Giardia 15.5kD protein binds the K-turn motif but not the variant K-loop motif. The highly conserved residues of loop 9, critical for RNA binding, also exhibit conformations similar to those of the human 15.5kD protein when bound to the K-turn motif. However, comparative sequence analysis indicated a distinct evolutionary position between Archaea and Eukarya. Indeed, assessment of the Giardia 15.5kD protein in denaturing experiments demonstrated an intermediate stability in protein structure when compared with that of the eukaryotic mouse 15.5kD and archaeal Methanocaldococcus jannaschii L7Ae proteins. Most notable was the ability of the Giardia 15.5kD protein to assemble in vitro a catalytically active chimeric box C/D RNP utilizing the archaeal M. jannaschii Nop56/58 and fibrillarin core proteins. In contrast, a catalytically competent chimeric RNP could not be assembled using the mouse 15.5kD protein. Collectively, these analyses suggest that the G. lamblia 15.5kD protein occupies a unique position in the evolution of this box C/D RNP core protein retaining structural and functional features characteristic of both archaeal L7Ae and higher eukaryotic 15.5kD homologues.

Download RCSB-PDB Structures:

Pdb Files   3O85.pdb  
Pdbx/mmCIF Files   3O85.cif  


Protein sequence:

MQIDPRAIPFANEELSLELLNLVKHGASLQAIKRGANEALKQVNRGKAELVIIAADADPIEIVLHLPLACEDKGVPYVFIGSKNALGRACNVSVPTIVASIGKHDALGNVVAEIVGKVEALV

Comments:

15.5kD protein is a homologue of yeast Snu13 and archaeal L7Ae. Binds to a common kink-turn motif of RNA. Together with Nop56, Nop58 and fibrillarine they make the core of the heteromeric C/D RNP complex. It is also part of the eukaryotic pre-mRNA splicesomal RNP apparatus. The crystal structure of the human homologue has been solved (PDB ID: 1E7K, 2OZB).





Alpha Fold Predicted Structure:






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Protein sequence:

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

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-A8BMJ0-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-A8BMJ0-F1.cif  
DSSP Secondary Structures   A8BMJ0.dssp  





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