3NVI

Structure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.709 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.

Xue, S.Wang, R.Yang, F.Terns, R.M.Terns, M.P.Zhang, X.Maxwell, E.S.Li, H.

(2010) Mol.Cell 39: 939-949

  • DOI: 10.1016/j.molcel.2010.08.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D R ...

    Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.


    Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NOP5/NOP56 related protein
A, C
379Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Find proteins for Q8U4M1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U4M1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
B, D
129Pyrococcus 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: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')E,F24Pyrococcus furiosus DSM 3638
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.709 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.216α = 90.00
b = 91.841β = 90.00
c = 155.603γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-07-08 
  • Released Date: 2011-07-20 
  • Deposition Author(s): Li, H., Xue, S., Wang, R.

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Derived calculations