4BY9

The structure of the Box CD enzyme reveals regulation of rRNA methylation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Structure of the Box C/D Enzyme Reveals Regulation of RNA Methylation.

Lapinaite, A.Simon, B.Skjaerven, L.Rakwalska-Bange, M.Gabel, F.Carlomagno, T.

(2013) Nature 502: 519

  • DOI: https://doi.org/10.1038/nature12581
  • Primary Citation of Related Structures:  
    4BY9

  • PubMed Abstract: 

    Post-transcriptional modifications are essential to the cell life cycle, as they affect both pre-ribosomal RNA processing and ribosome assembly. The box C/D ribonucleoprotein enzyme that methylates ribosomal RNA at the 2'-O-ribose uses a multitude of guide RNAs as templates for the recognition of rRNA target sites. Two methylation guide sequences are combined on each guide RNA, the significance of which has remained unclear. Here we use a powerful combination of NMR spectroscopy and small-angle neutron scattering to solve the structure of the 390 kDa archaeal RNP enzyme bound to substrate RNA. We show that the two methylation guide sequences are located in different environments in the complex and that the methylation of physiological substrates targeted by the same guide RNA occurs sequentially. This structure provides a means for differential control of methylation levels at the two sites and at the same time offers an unexpected regulatory mechanism for rRNA folding.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NOP5/NOP56 RELATED PROTEIN
C, F, I, L
366Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U4M1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U4M1
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UniProt GroupQ8U4M1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AE
D, G, J, M
121Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
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UniProt GroupQ8U160
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
E, H, K, N
227Pyrococcus furiosusMutation(s): 0 
EC: 2.1.1
UniProt
Find proteins for Q8U4M2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U4M2 
Go to UniProtKB:  Q8U4M2
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UniProt GroupQ8U4M2
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Entity ID: 1
MoleculeChains LengthOrganismImage
SSR26
A, B
72Pyrococcus furiosus
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'O [auth W],
P [auth X],
Q [auth Y],
R [auth Z]
11Pyrococcus furiosus
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Atomic model
  • Version 1.2: 2013-10-23
    Changes: Database references
  • Version 1.3: 2013-10-30
    Changes: Database references
  • Version 1.4: 2016-05-04
    Changes: Atomic model, Other
  • Version 1.5: 2023-06-14
    Changes: Data collection, Database references, Other