3NVK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.209 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.0 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, F
376Pyrococcus 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
E, H
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
MoleculeChainsSequence LengthOrganismDetails
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
I, J
234Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: flpA
EC: 2.1.1.-
Find proteins for Q8U4M2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U4M2
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*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')K,L34N/A
Entity ID: 5
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')G,S13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
I, J
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.209 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 330.039α = 90.00
b = 94.548β = 90.00
c = 97.729γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building
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): Xue, S., Wang, R., Li, H.

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release