5GIN

Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Literature

Box C/D guide RNAs recognize a maximum of 10 nt of substrates

Yang, Z.Lin, J.Ye, K.

(2016) Proc Natl Acad Sci U S A 113: 10878-10883

  • DOI: https://doi.org/10.1073/pnas.1604872113
  • Primary Citation of Related Structures:  
    5GIN, 5GIO, 5GIP

  • PubMed Abstract: 

    Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.


  • Organizational Affiliation

    College of Biological Sciences, China Agricultural University, Beijing 100193, China; National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, 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 subunitA,
D [auth B],
M [auth K]
388Saccharolobus solfataricusMutation(s): 0 
Gene Names: SULA_1947SULB_1948SULC_1946
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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeB [auth C],
E [auth D],
N [auth L]
130Saccharolobus solfataricusMutation(s): 0 
Gene Names: rpl7aeSULA_1106SULB_1107SULC_1105
UniProt
Find proteins for P55858 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Go to UniProtKB:  P55858
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UniProt GroupP55858
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseC [auth E],
F,
O [auth M]
232Saccharolobus solfataricusMutation(s): 0 
Gene Names: flpASSOP1_0970SULA_1948SULB_1949SULC_1947
EC: 2.1.1
UniProt
Find proteins for P58032 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P58032 
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UniProt GroupP58032
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
C/D RNAG,
H,
K [auth N]
40Saccharolobus solfataricus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
substrateI,
J,
L [auth O]
9Saccharolobus solfataricus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.676α = 90
b = 242.676β = 90
c = 146.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description