3MQK

Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA trinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 

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This is version 1.1 of the entry. See complete history


Literature

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide.

Zhou, J.Liang, B.Li, H.

(2011) RNA 17: 244-250

  • DOI: 10.1261/rna.2415811
  • Primary Citation of Related Structures:  
    3MQK

  • PubMed Abstract: 
  • Cbf5 is the catalytic subunit of the H/ACA small nucleolar/Cajal body ribonucleoprotein particles (RNPs) responsible for site specific isomerization of uridine in ribosomal and small nuclear RNA. Recent evidence from studies on archaeal Cbf5 suggests its second functional role in modifying tRNA U55 independent of guide RNA ...

    Cbf5 is the catalytic subunit of the H/ACA small nucleolar/Cajal body ribonucleoprotein particles (RNPs) responsible for site specific isomerization of uridine in ribosomal and small nuclear RNA. Recent evidence from studies on archaeal Cbf5 suggests its second functional role in modifying tRNA U55 independent of guide RNA. In order to act both as a stand-alone and a RNP pseudouridine synthase, Cbf5 must differentiate features in H/ACA RNA from those in tRNA or rRNA. Most H/ACA RNAs contain a hallmark ACA trinucleotide downstream of the H/ACA motif. Here we challenged an archaeal Cbf5 (in the form of a ternary complex with its accessory proteins Nop10 and Gar1) with T-stem-loop RNAs with or without ACA trinucleotide in the stem. Although these substrates were previously shown to be substrates for the bacterial stand-alone pseudouridine synthase TruB, the Cbf5-Nop10-Gar1 complex was only able to modify those without ACA trinucleotide. A crystal structure of Cbf5-Nop10-Gar1 trimer bound with an ACA-containing T-stem-loop revealed that the ACA trinucleotide detracted Cbf5 from the stand-alone binding mode, thereby suggesting that the H/ACA RNP-associated function of Cbf5 likely supersedes its stand-alone function.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA pseudouridine synthase BA328Pyrococcus furiosusMutation(s): 0 
Gene Names: truBPF1785
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 Nop10B52Pyrococcus 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
Small nucleolar rnp gar1-like proteinC75Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1791
UniProt
Find proteins for Q8U029 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U029 
Go to UniProtKB:  Q8U029
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UniProt GroupQ8U029
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3')D 13N/A
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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*GP*AP*UP*CP*CP*AP*CP*A)-3')E 9N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.696α = 90
b = 105.696β = 90
c = 243.925γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance