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



Literature

Nop9 recognizes structured and single-stranded RNA elements of pre-ribosomal RNA.

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

(2020) RNA 

  • DOI: 10.1261/rna.075416.120
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nop9 is an essential factor in the processing of pre-ribosomal 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 a ...

    Nop9 is an essential factor in the processing of pre-ribosomal 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 pre-ribosomal RNA. This structure reveals that Nop9 brings together a C-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional N-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 N- and C-terminal modules retain the characteristic sequence-specific recognition of PUF proteins but the N-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

    NIEHS, NIH; hall4@niehs.nih.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 9
A
591Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP9YJL010CJ1357
Find proteins for P47077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47077

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
RNA (47-MER)B, C47Saccharomyces cerevisiae S288C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCE
Query on TCE

Download CCD File 
A
3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
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 

  • Version 1.0: 2020-05-20
    Type: Initial release