7XPL

Crystal structure of a C/D-free RNA-guided RNA 2'-O-methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Literature

Methylation guide RNAs without box C/D motifs.

Wang, J.Yang, Z.Ye, K.

(2022) RNA 28: 1597-1605

  • DOI: https://doi.org/10.1261/rna.079379.122
  • Primary Citation of Related Structures:  
    7XPL

  • PubMed Abstract: 

    Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The defining feature of methylation guide RNAs is two sets of box C and D motifs that form kink-turn structures specifically recognized by L7Ae family proteins. Here, we engineered a new type of methylation guide that lacks C/D motifs and requires no L7Ae for assembly and function. We determined a crystal structure of a bipartite C/D-free guide RNA in complex with Nop5, fibrillarin and substrate in the active form at 2.2 Å resolution. The stems of new guide RNAs functionally replace C/D motifs in Nop5 binding, precisely placing the substrate for site-specific modification. We also found that the bipartite architecture and association of L7Ae with C/D motifs enhance modification when association of guide RNAs or substrates is weak. Our study provides insights into the variations, robustness and possible evolutionary path of methylation guide RNAs.


  • Organizational Affiliation

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
A, B
388Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for Q97ZH3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97ZH3 
Go to UniProtKB:  Q97ZH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97ZH3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseC [auth E],
D [auth F]
232Saccharolobus solfataricus 98/2Mutation(s): 0 
Gene Names: flpASsol_1916
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58032
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
BMG3 RNA strand AE [auth G]29Saccharolobus solfataricus
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Entity ID: 4
MoleculeChains LengthOrganismImage
BMG3 RNA strand BF [auth H]29Saccharolobus solfataricus
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*UP*U)-3')G [auth I],
H [auth J]
11Saccharolobus solfataricus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.088α = 92.86
b = 76.185β = 94.08
c = 98.201γ = 112.91
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description