Modomics - A Database of RNA Modifications

ID Card:

Full name: H/ACA ribonucleoprotein complex subunit 1
GI: 120941
Orf: YHR089C
COG: COG3277
UniProt: P28007
Structures: | 3UAI | 3U28 |
Alpha Fold Predicted Structure: AF-P28007-F1
Complex: H/ACA RNP


PDB Structures:


3UAI

Structure Description:

Title: Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Classification: ISOMERASE/PROTEIN BINDING
Technique: X-Ray Diffraction
Resolution: 1.9
R value free: 0.233
R value observed: 0.205
R value work: 0.204

Abstract of the PDB Structure's related Publication:

Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functional Saccharomyces cerevisiae H/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1.9 Å resolution; and analyzed the structure-function relationship of the yeast complex. Although eukaryotic H/ACA RNAs have a conserved two-hairpin structure, isolated single-hairpin RNAs are also active in guiding pseudouridylation. Nhp2, unlike its archaeal counterpart, is largely dispensable for the activity, reflecting a functional adaptation of eukaryotic H/ACA RNPs to the variable RNA structure that Nhp2 binds. The N-terminal extension of Cbf5, a hot spot for dyskeratosis congenita mutation, forms an extra structural layer on the PUA domain. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1-Naf1 exchange during H/ACA RNP maturation. Our results reveal significant novel features of eukaryotic H/ACA RNPs.

Download RCSB-PDB Structures:

Pdb Files   3U28.pdb   3UAI.pdb  
Pdbx/mmCIF Files   3U28.cif   3UAI.cif  


Protein sequence:

MSFRGGNRGGRGGFRGGFRGGRTGSARSFQQGPPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGDKFYIAADKLLPIERFLPKPKVVGPPKPKNKKKRSGAPGGRGGASMGRGGSRGGFRGGRGGSSFRGGRGGSSFRGGSRGGSFRGGSRGGSRGGFRGGRR

Comments:

Essential subunit of the nucleolar Box H/ACA ribonucleoprotein particles (RNP) involved in 2’-O-methylation of several cellular RNA (mainly rRNA and snRNA), including intron-containing pre-RNA in yeast. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1-Naf1 exchange during H/ACA RNP maturation.





Alpha Fold Predicted Structure:




Parsing response... [182153/182153]


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Protein sequence:

M S F R G G N R G G R G G F R G G F R G G R T G S A R S F Q Q G P P D T V L E M G A F L H P C E G D I V C R S I N T K I P Y F N A P I Y L E N K T Q V G K V D E I L G P L N E V F F T I K C G D G V Q A T S F K E G D K F Y I A A D K L L P I E R F L P K P K V V G P P K P K N K K K R S G A P G G R G G A S M G R G G S R G G F R G G R G G S S F R G G R G G S S F R G G S R G G S F R G G S R G G S R G G F R G G R R
20406080100120140160180200MSFRGGNRGGRGGFRGGFRGGRTGSARSFQQGPPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGDKFYIAADKLLPIERFLPKPKVVGPPKPKNKKKRSGAPGGRGGASMGRGGSRGGFRGGRGGSSFRGGRGGSSFRGGSRGGSFRGGSRGGSRGGFRGGRRSequenceGTSN

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-P28007-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P28007-F1.cif  
DSSP Secondary Structures   P28007.dssp  





Publications:

Links:

_PubMed_
_SGD_
_Wikipedia - Small nucleolar RNA_