Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.55 kDa 
• Atom Count: 2494 
• Modelled Residue Count: 310 
• Deposited Residue Count: 318 
• Unique protein chains: 1

4MJ7

Crystal structure of the PIN domain of Saccharomyces cerevisiae Utp23

• PDB DOI: 10.2210/pdb4MJ7/pdb

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


• Deposited: 2013-09-03 Released: 2013-11-06 
• Deposition Author(s): Lu, J., Ye, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.288 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain

Lu, J., Sun, M., Ye, K.

(2013) RNA 19: 1815-1824

• PubMed: 24152547 
• DOI: 10.1261/rna.040808.113
• Primary Citation of Related Structures:  
  4MJ7


• PubMed Abstract: 
  

During synthesis of yeast ribosome, a large complex, called the 90S pre-ribosome or the small subunit processome, is assembled on the nascent precursor rRNA and mediates early processing of 18S rRNA. The Utp23 protein and snR30 H/ACA snoRNA are two conserved components of 90S pre-ribosomes. Utp23 contains a degenerate PIN nuclease domain followed by a long C-terminal tail and associates specifically with snR30. Here, we report the crystal structure of the Utp23 PIN domain at 2.5-Å resolution. The structure reveals a conserved core fold of PIN domain with degenerate active site residues, a unique CCHC Zn-finger motif, and two terminal extension elements. Functional sites of Utp23 have been examined with conservation analysis, mutagenesis, and in vivo and in vitro assays. Mutations in each of three cysteine ligands of zinc, although not the histidine ligand, were lethal or strongly inhibitory to yeast growth, indicating that the Zn-finger motif is required for Utp23 structure or function. The N-terminal helix extension harbors many highly conserved basic residues that mostly are critical for growth and in vitro RNA-binding activity of Utp23. Deletion of the C-terminal tail, which contains a short functionally important sequence motif, disrupted the interaction of Utp23 with snR30 and perturbed the pre-ribosomal association of Utp23. Our data establish a structural framework for dissecting Utp23 function in the assembly and dynamics of 90S pre-ribosomes.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein UTP23	A, B	159	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UTP23, YOR004W
UniProt
Find proteins for Q12339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12339  Go to UniProtKB:  Q12339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.288 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.427	α = 90
b = 91.427	β = 90
c = 92.26	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-03 
• Released Date: 2013-11-06 
Deposition Author(s): Lu, J., Ye, K.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references