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 
  • R-Value Observed: 0.218 

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:  
    3HJW, 3HJY

  • 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 partially understood ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pseudouridine synthase Cbf5A327Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1785
EC: 5.4.99 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q7LWY0 
Go to UniProtKB:  Q7LWY0
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UniProt GroupQ7LWY0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop10B53Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1141
UniProt
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1R4 
Go to UniProtKB:  Q8U1R4
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UniProt GroupQ8U1R4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC120Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1367rpl7ae
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
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UniProt GroupQ8U160
Protein Feature View
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Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (58-MER)D 58N/A
Protein Feature View
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5'-R(*GP*AP*GP*CP*GP*(FHU)P*GP*CP*GP*GP*UP*UP*U)-3'E 13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
G [auth E]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.013α = 90
b = 63.026β = 90
c = 85.447γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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