Modomics - A Database of RNA Modifications

ID Card:

Full name: 50S ribosomal protein L7Ae
Synonym: rpl7ae, SSO0091
GI: 15897054
Orf: C04_031
COG: COG1358
UniProt: P55858
Structures: | 3ICX | 3ID5 | 3ID6 |
Alpha Fold Predicted Structure: AF-P55858-F1
Complex: C/D RNP


PDB Structures:


3ICX

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.

Download RCSB-PDB Structures:

Pdb Files   3ICX.pdb   3ID5.pdb   3ID6.pdb  
Pdbx/mmCIF Files   3ICX.cif   3ID5.cif   3ID6.cif  


Protein sequence:

MNAMSKASYVKFEVPQDLADKVLEAVRKAKESGKIKKGTNETTKAVERGQAKLVIIAEDVQPEEIVAHLPLLCDEKKIPYVYVSSKKALGEACGLQVATASAAILEPGEAKDLVDEIIKRVNEIKGKTSS

Comments:

L7Ae protein, together with fused Nop56/58 (also designated Nop5) and Fibrillarin methyltranferase (FlpA), makes the core of C/D RNP complex in Archaea. It is a homologue of S. cerevisiae Snu13 and mammalian 15.5kD protein. Archaeal L7Ae is also a subunit of H/ACA RNP complex, a subunit of RNase P and one of the ribosomal protein of the 50S subunit. In all cases L7Ae binds to a common kink-turn motif of RNA.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P55858-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P55858-F1.cif  
DSSP Secondary Structures   P55858.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural organization of box C/D RNA-guided RNA methyltransferase. Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L Proc Natl Acad Sci U S A [details] 19666563 -
Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K Nature [details] 21270896 -

Links:

_PubMed_