3PLA

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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Literature

Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.

Lin, J.Lai, S.Jia, R.Xu, A.Zhang, L.Lu, J.Ye, K.

(2011) Nature 469: 559-563

  • DOI: https://doi.org/10.1038/nature09688
  • Primary Citation of Related Structures:  
    3PLA

  • PubMed Abstract: 

    Box C/D RNA protein complexes (RNPs) direct site-specific 2'-O-methylation of RNA and ribosome assembly. The guide RNA in C/D RNP forms base pairs with complementary substrates and selects the modification site using a molecular ruler. Despite many studies of C/D RNP structure, the fundamental questions of how C/D RNAs assemble into RNPs and how they guide modification remain unresolved. Here we report the crystal structure of an entire catalytically active archaeal C/D RNP consisting of a bipartite C/D RNA associated with two substrates and two copies each of Nop5, L7Ae and fibrillarin at 3.15-Å resolution. The substrate pairs with the second through the eleventh nucleotide of the 12-nucleotide guide, and the resultant duplex is bracketed in a channel with flexible ends. The methyltransferase fibrillarin binds to an undistorted A-form structure of the guide-substrate duplex and specifically loads the target ribose into the active site. Because interaction with the RNA duplex alone does not determine the site specificity, fibrillarin is further positioned by non-specific and specific protein interactions. Compared with the structure of the inactive C/D RNP, extensive domain movements are induced by substrate loading. Our results reveal the organization of a monomeric C/D RNP and the mechanism underlying its site-specific methylation activity.


  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing 102206, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre mRNA splicing protein
A, B, K
388Saccharolobus solfataricusMutation(s): 1 
Gene Names: SSO0939
UniProt
Find proteins for Q97ZH3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Go to UniProtKB:  Q97ZH3
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UniProt GroupQ97ZH3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7Ae
C, D, L
130Saccharolobus solfataricus 98/2Mutation(s): 1 
Gene Names: rpl7aeSsol_1068
UniProt
Find proteins for D0KRE2 (Saccharolobus solfataricus (strain 98/2))
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Go to UniProtKB:  D0KRE2
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UniProt GroupD0KRE2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
E, F, M
232Saccharolobus solfataricusMutation(s): 1 
Gene Names: flpASSO0940C33_014
EC: 2.1.1
UniProt
Find proteins for P58032 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P58032 
Go to UniProtKB:  P58032
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UniProt GroupP58032
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
C/D guide RNA
G, H, N
40synthetic construct
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')
I, J, O
10synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.199α = 90
b = 241.199β = 90
c = 145.408γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description