2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes

Scarsdale, J.N.Peculis, B.A.Wright, H.T.

(2006) Structure 14: 331-343

  • DOI: https://doi.org/10.1016/j.str.2005.11.010
  • Primary Citation of Related Structures:  
    2A8P, 2A8Q, 2A8R, 2A8S, 2A8T

  • PubMed Abstract: 

    X29, a 25 kDa Nudix hydrolase from Xenopus laevis that cleaves 5' caps from U8 snoRNA, crystallizes as a homodimeric apoenzyme. Manganese binds crystals of apo-X29 to form holo-X29 only in the presence of nucleot(s)ide. Structural changes in X29 on nucleo-t(s)ide-assisted Mn(+2) uptake account for the observed cooperativity of metal binding. Structures of X29 with GTP or m7GpppA show a different mode of ligand binding from that of other cap binding proteins and suggest a possible three- or four-metal Nudix reaction mechanism. The X29 dimer has no known RNA binding motif, but its striking surface dipolarity and unique structural features create a plausible RNA binding channel on the positive face of the protein. Because U8 snoRNP is essential for accumulation of mature 5.8S and 28S rRNA in vertebrate ribosome biogenesis, and cap structures are required for U8 stability in vivo, X29 could profoundly influence this fundamental cellular pathway.

  • Organizational Affiliation

    Department of Biochemistry and Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, Virginia 23219, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U8 snoRNA-binding protein X29
A, B
212Xenopus laevisMutation(s): 0 
EC: 3.6.1
Find proteins for Q6TEC1 (Xenopus laevis)
Explore Q6TEC1 
Go to UniProtKB:  Q6TEC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TEC1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MGT

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
C11 H20 N5 O14 P3
Query on ADN

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
C10 H13 N5 O4
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.702α = 90
b = 81.71β = 90
c = 111.706γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description