2RFK

Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.

Liang, B.Xue, S.Terns, R.M.Terns, M.P.Li, H.

(2007) Nat Struct Mol Biol 14: 1189-1195

  • DOI: 10.1038/nsmb1336
  • Primary Citation of Related Structures:  
    2RFK

  • PubMed Abstract: 
  • The most complex RNA pseudouridylases are H/ACA ribonucleoprotein particles, which use a guide RNA for substrate capture and four proteins (Cbf5, Nop10, Gar1 and L7Ae/NHP2) for substrate modification. Here we report the three-dimensional structure of a catalytically deficient archaeal enzyme complex (including the guide RNA and three of the four essential proteins) bound to a substrate RNA ...

    The most complex RNA pseudouridylases are H/ACA ribonucleoprotein particles, which use a guide RNA for substrate capture and four proteins (Cbf5, Nop10, Gar1 and L7Ae/NHP2) for substrate modification. Here we report the three-dimensional structure of a catalytically deficient archaeal enzyme complex (including the guide RNA and three of the four essential proteins) bound to a substrate RNA. Extensive interactions of Cbf5 with one guide-substrate helix and a guide RNA stem shape the forked guide–substrate RNA complex structure and position the substrate in proximity of the Cbf5 catalytic center. Our structural and complementary fluorescence analyses also indicate that precise placement of the target uridine at the active site requires a conformation of the guide–substrate RNA duplex that is brought about by the previously identified concurrent interaction of the guide RNA with L7Ae and a composite Cbf5-Nop10 surface, and further identify a residue that is critical in this process.


    Organizational Affiliation

    Institute of Molecular Biophysics, 91 Chiefton Way, Florida State University, Tallahasee, Florida 32306, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Probable tRNA pseudouridine synthase BD [auth A]334Pyrococcus furiosusMutation(s): 1 
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))
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Go to UniProtKB:  Q7LWY0
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UniProt GroupQ7LWY0
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop10E [auth B]53Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U1R4
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UniProt GroupQ8U1R4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nucleolar rnp similar to gar1F [auth C]74Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U029 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U029
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UniProt GroupQ8U029
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Entity ID: 1
MoleculeChainsLengthOrganismImage
guide RNA 1A [auth D]21N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
guide RNA 2B [auth E]26N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
target RNAC [auth F]14N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.561α = 90
b = 96.561β = 90
c = 240.978γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations