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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This is version 1.2 of the entry. See complete history


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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Pre mRNA splicing proteinA, B, K388Saccharolobus 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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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC, D, L130Saccharolobus 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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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseE, F, M232Saccharolobus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
C/D guide RNAG, H, N40synthetic construct
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')I, J, O10synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAH (Subject of Investigation/LOI)
    Query on SAH

    Download Ideal Coordinates CCD File 
    P [auth E], Q [auth F], R [auth M]S-ADENOSYL-L-HOMOCYSTEINE
    C14 H20 N6 O5 S
    ZJUKTBDSGOFHSH-WFMPWKQPSA-N
     Ligand Interaction
    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