6WPI

Crystal structure of Nop9 in complex with ITS1 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA.

Zhang, J.Teramoto, T.Qiu, C.Wine, R.N.Gonzalez, L.E.Baserga, S.J.Tanaka Hall, T.M.

(2020) RNA 26: 1049-1059

  • DOI: 10.1261/rna.075416.120
  • Primary Citation of Related Structures:  
    6WPI

  • PubMed Abstract: 
  • Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA ...

    Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA-Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.


    Organizational Affiliation

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 9A591Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP9YJL010CJ1357
UniProt
Find proteins for P47077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47077 
Go to UniProtKB:  P47077
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (47-MER)B, C47Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCE
Query on TCE

Download Ideal Coordinates CCD File 
D [auth A]3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.925α = 90
b = 119.54β = 90
c = 142.047γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA5016

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references