Modomics - A Database of RNA Modifications

ID Card:

Full name: 13 kDa ribonucleoprotein-associated protein
Synonym: YEL026W
GI: 731411
Orf: YEL026W
COG: COG1358
UniProt: P39990
Structures: | 2ALE | 1ZWZ | 3JCM | 4NUT | 5GAN | 5GAP | 5NRL | 5TZS | 5WLC | 5WYJ | 5WYK | 5ZWM | 5ZWO | 6KE6 | 6LQP | 6LQQ | 6LQR | 6LQS | 6LQT | 6LQU | 6LQV | 6ND4 | 6ZQA | 6ZQB | 6ZQC | 6ZQD | 6ZQE | 7AJT | 7AJU | 7D4I | 7D5S | 7D5T | 7D63 |
Alpha Fold Predicted Structure: AF-P39990-F1
Complex: C/D RNP


PDB Structures:


2ALE

Structure Description:

Title: Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 1.90
R value free: 0.209
R value observed: 0.184
R value work: 0.183

Abstract of the PDB Structure's related Publication:

Snu13p is a bifunctional yeast protein involved in both messenger RNA splicing as well as ribosomal RNA maturation. Snu13p initiates assembly of ribonucleoprotein particles by interacting with a conserved RNA motif called kink turn. Unlike its archaeal homolog, L7Ae, Snu13p displays differential specificity for functionally distinct kink turns. Thus, the structures of Snu13p at different functional states, including those alone and bound with RNAs, are required to understand how the protein differentially interacts with kink turns. Although the structure of the human homolog of Snu13p bound with a spliceosomal RNA is known, there has not been a report of a structure of free Snu13p. This has hindered our ability to understand the structural basis for Snu13p's substrate specificity. We report a crystal structure of free Snu13p at 1.9A and a detailed structural comparison with its homologs. We show that free Snu13p has nearly an identical conformation as that of its human homolog bound with RNA. Interestingly, both eukaryotic proteins exhibit notable structural differences in their central beta-sheets as compared to their archaeal homolog, L7Ae. The observed structural differences offer a possible explanation to the observed difference in RNA specificity between Snu13p and L7Ae.

Download RCSB-PDB Structures:

Pdb Files   1ZWZ.pdb   2ALE.pdb   3JCM.pdb   4NUT.pdb   5GAN.pdb   5GAP.pdb   5TZS.pdb   5ZWO.pdb   6LKP.pdb   6ND4.pdb   7AJT.pdb  
Pdbx/mmCIF Files   1ZWZ.cif   2ALE.cif   3JCM.cif   4NUT.cif   5GAN.cif   5GAP.cif   5NRL.cif   5TZS.cif   5WLC.cif   5WYJ.cif   5WYK.cif   5ZWM.cif   5ZWO.cif   6KE6.cif   6LKP.cif   6LQQ.cif   6LQR.cif   6LQS.cif   6LQT.cif   6LQU.cif   6LQV.cif   6ND4.cif   6ZQA.cif   6ZQB.cif   6ZQC.cif   6ZQD.cif   6ZQE.cif   7AJT.cif   7D4I.cif   7D5S.cif   7D5T.cif   7D63.cif  


Protein sequence:

MSAPNPKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQIYAVKDKIETLLI

Comments:

Snu13 protein together with Nop56 and Nop58 makes the core of C/D RNP complex in yeast. It is a homologue of mammalian 15.5kD protein and Archaea L7Ae.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P39990-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P39990-F1.cif  
DSSP Secondary Structures   P39990.dssp  





Publications:

Links:

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