5WTX

Structure of Nop9

• PDB DOI: https://doi.org/10.2210/pdb5WTX/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-15 Released: 2017-01-25 
• Deposition Author(s): Ye, K., Wang, B.
• Funding Organization(s): National Natural Science Foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Literature

Nop9 binds the central pseudoknot region of 18S rRNA

Wang, B., Ye, K.

(2017) Nucleic Acids Res 45: 3559-3567

• PubMed: 28053123 
• DOI: https://doi.org/10.1093/nar/gkw1323
• Primary Citation of Related Structures:  
  5WTX, 5WTY


• PubMed Abstract: 
  

  The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.84 kDa 
• Atom Count: 4,460 
• Modelled Residue Count: 543 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 9	A	666	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NOP9
UniProt
Find proteins for P47077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47077  Go to UniProtKB:  P47077

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.801	α = 90
b = 134.846	β = 90
c = 145.921	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Ye, K., Wang, B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31430024
National Natural Science Foundation of China	China	31325007
National Natural Science Foundation of China	China	91540201
Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08010203

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references