Modomics - A Database of RNA Modifications

ID Card:

Full name: 50S ribosomal protein L7Ae
Synonym: rpl7ae, PF1367
GI: 18977739
COG: COG1358
UniProt: Q8U160
Structures: | 3NMU |
Alpha Fold Predicted Structure: AF-Q8U160-F1
Complex: C/D RNP


PDB Structures:


3NMU

Structure Description:

Title: Crystal Structure of substrate-bound halfmer box C/D RNP
Classification: Transferase/RNA
Technique: X-Ray Diffraction
Resolution: 2.73
R value free: 0.284
R value observed: 0.224
R value work: 0.222

Abstract of the PDB Structure's related Publication:

Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.

Download RCSB-PDB Structures:

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


Protein sequence:

MMAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK

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:




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Protein sequence:

M M A K P S Y V K F E V P K E L A E K A L Q A V E I A R D T G K I R K G T N E T T K A V E R G Q A K L V I I A E D V D P E E I V A H L P P L C E E K E I P Y I Y V P S K K E L G A A A G I E V A A A S V A I I E P G K A R D L V E E I A M K V K E L M K
102030405060708090100110120MMAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMKSequenceGHTSN

Enter the variants

Position

Original

Variant

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-Q8U160-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8U160-F1.cif  
DSSP Secondary Structures   Q8U160.dssp  





Publications:

Links:

_PubMed_