3HJW

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

Liang, B.Zhou, J.Kahen, E.Terns, R.M.Terns, M.P.Li, H.

(2009) Nat.Struct.Mol.Biol. 16: 740-746

  • DOI: 10.1038/nsmb.1624
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only ...

    Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 A of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.


    Organizational Affiliation

    Institute of Molecular Biophysics, Tallahassee, Florida, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pseudouridine synthase Cbf5
A
327Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: truB
EC: 5.4.99.25
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q7LWY0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein Nop10
B
53Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: nop10
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1R4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
C
120Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U160
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (58-MER)D58N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-R(*GP*AP*GP*CP*GP*(FHU)P*GP*CP*GP*GP*UP*UP*U)-3'E13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FHU
Query on FHU
E
RNA LINKINGC9 H14 F N2 O10 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 186.013α = 90.00
b = 63.026β = 90.00
c = 85.447γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2015-08-12
    Type: Refinement description
  • Version 1.3: 2017-11-01
    Type: Refinement description