4NSX

Crystal Structure of the Utp21 tandem WD Domain


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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21A684Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: L8084.22UTP21YLR409C
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06078 
Go to UniProtKB:  Q06078
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
B [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
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 = 35.493α = 110.95
b = 63.54β = 95.83
c = 82.549γ = 97.93
Software Package:
Software NamePurpose
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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