Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 76.28 kDa 
• Atom Count: 5381 
• Modelled Residue Count: 634 
• Deposited Residue Count: 684 
• Unique protein chains: 1

4NSX

Crystal Structure of the Utp21 tandem WD Domain

• PDB DOI: 10.2210/pdb4NSX/pdb

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


• Deposited: 2013-11-29 Released: 2014-02-19 
• Deposition Author(s): Zhang, C., Ye, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structure of Utp21 Tandem WD Domain Provides Insight into the Organization of the UTPB Complex Involved in Ribosome Synthesis

Zhang, C., Lin, J., Liu, W., Chen, X., Chen, R., Ye, K.

(2014) PLoS One 9: e86540-e86540

• PubMed: 24466140 
• DOI: 10.1371/journal.pone.0086540
• Primary Citation of Related Structures:  
  4NSX


• PubMed Abstract: 
  

Assembly of the eukaryotic ribosome requires a large number of trans-acting proteins and small nucleolar RNAs that transiently associate with the precursor rRNA to facilitate its modification, processing and binding with ribosomal proteins. UTPB is a large evolutionarily conserved complex in the 90S small subunit processome that mediates early processing of 18S rRNA. UTPB consists of six proteins Utp1/Pwp1, Utp6, Utp12/Dip2, Utp13, Utp18 and Utp21 and has abundant WD domains. Here, we determined the crystal structure of the tandem WD domain of yeast Utp21 at 2.1 Å resolution, revealing two open-clamshell-shaped β-propellers. The bottom faces of both WD domains harbor several conserved patches that potentially function as molecular binding sites. We show that residues 100-190 of Utp18 bind to the tandem WD domain of Utp21. Structural mapping of previous crosslinking data shows that the WD domains of Utp18 and Utp1 are organized on two opposite sides of the Utp21 WD domains. This study reports the first structure of a UTPB component and provides insight into the structural organization of the UTPB complex.

---

Organizational Affiliation: 

National Institute of Biological Sciences, Beijing, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 21	A	684	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: L8084.22, UTP21, YLR409C
UniProt
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06078  Go to UniProtKB:  Q06078

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	B [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.493	α = 110.95
b = 63.54	β = 95.83
c = 82.549	γ = 97.93

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: 2013-11-29 
• Released Date: 2014-02-19 
Deposition Author(s): Zhang, C., Ye, K.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release