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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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 ...

    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 guideā€“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 guideā€“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

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Probable tRNA pseudouridine synthase B
A
334Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 1 
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: 5
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: 6
MoleculeChainsSequence LengthOrganismDetails
Small nucleolar rnp similar to gar1
C
74Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Find proteins for Q8U029 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U029
Entity ID: 1
MoleculeChainsLengthOrganism
guide RNA 1D21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
guide RNA 2E26N/A
Entity ID: 3
MoleculeChainsLengthOrganism
target RNAF14N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
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 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.561α = 90.00
b = 96.561β = 90.00
c = 240.978γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance