Structural Characterization of Nop10p using Nuclear Magnetic Resonance Spectroscopy

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.4 of the entry. See complete history


Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA

Khanna, M.Wu, H.Johansson, C.Caizergues-Ferrer, M.Feigon, J.

(2006) RNA 12: 40-52

  • DOI: https://doi.org/10.1261/rna.2221606
  • Primary Citation of Related Structures:  
    1Y2Y, 2EUY

  • PubMed Abstract: 

    The H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes guide the modification of uridine to pseudouridine at conserved sites in rRNA. The H/ACA snoRNPs each comprise a target-site-specific snoRNA and four core proteins, Nop10p, Nhp2p, Gar1p, and the pseudouridine synthase, Cbf5p, in yeast. The secondary structure of the H/ACA snoRNAs includes two hairpins that each contain a large internal loop (the pseudouridylation pocket), one or both of which are partially complementary to the target RNA(s). We have determined the solution structure of an RNA hairpin derived from the human U65 box H/ACA snoRNA including the pseudouridylation pocket and adjacent stems, providing the first three-dimensional structural information on these H/ACA snoRNAs. We have also determined the structure of Nop10p and investigated its interaction with RNA using NMR spectroscopy. Nop10p contains a structurally well-defined N-terminal region composed of a beta-hairpin, and the rest of the protein lacks a globular structure. Chemical shift mapping of the interaction of RNA constructs of U65 box H/ACA 3' hairpin with Nop10p shows that the beta-hairpin binds weakly but specifically to RNA. The unstructured region of Nop10p likely interacts with Cbf5p.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, 607 Charles Young Drive East, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop1058Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NOP10
Find proteins for Q6Q547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q6Q547 
Go to UniProtKB:  Q6Q547
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Q547
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection