3ID5

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.01 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural organization of box C/D RNA-guided RNA methyltransferase.

Ye, K.Jia, R.Lin, J.Ju, M.Peng, J.Xu, A.Zhang, L.

(2009) Proc Natl Acad Sci U S A 106: 13808-13813

  • DOI: 10.1073/pnas.0905128106
  • Primary Citation of Related Structures:  
    3ICX, 3ID5, 3ID6

  • PubMed Abstract: 
  • Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity ...

    Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing 102206, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre mRNA splicing proteinA, E388Saccharolobus solfataricusMutation(s): 1 
Gene Names: SSO0939
UniProt
Find proteins for Q97ZH3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97ZH3 
Go to UniProtKB:  Q97ZH3
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UniProt GroupQ97ZH3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferaseB, F232Saccharolobus 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeC, G130Saccharolobus solfataricusMutation(s): 0 
Gene Names: rpl7aeSSO0091C04_031
UniProt
Find proteins for P55858 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P55858 
Go to UniProtKB:  P55858
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UniProt GroupP55858
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
half C/D RNAD, H 35N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
I [auth B],
J [auth F]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.01 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.485α = 90
b = 265.485β = 90
c = 129.434γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2009-07-20 
  • Released Date: 2009-08-25 
  • Deposition Author(s): Ye, K.

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations