4ADV

Structure of the E. coli methyltransferase KsgA bound to the E. coli 30S ribosomal subunit

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 of the entry. See complete history. 


Literature

Structural Insights Into Methyltransferase Ksga Function in 30S Ribosomal Subunit Biogenesis

Boehringer, D., O'Farrell, H.C., Rife, J.P., Ban, N.

(2012) J Biol Chem 287: 10453-10459

  • DOI: https://doi.org/10.1074/jbc.M111.318121
  • Primary Citation of Related Structures:  
    4ADV

  • PubMed Abstract: 

    • The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis ...

    The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.

    Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland, and. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B240Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C232Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D205Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E166Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G178Escherichia coliMutation(s): 0 
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S8H129Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S9I129Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S10J103Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11K128Escherichia coliMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S12L123Escherichia coliMutation(s): 0 
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13M117Escherichia coliMutation(s): 0 
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S14N100Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S15O89Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S16P82Escherichia coliMutation(s): 0 
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S17Q83Escherichia coliMutation(s): 0 
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S18R74Escherichia coliMutation(s): 0 
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S19S91Escherichia coliMutation(s): 0 
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S20T86Escherichia coliMutation(s): 0 
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Entity ID: 21
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30S RIBOSOMAL PROTEIN S21U71Escherichia coliMutation(s): 0 
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Entity ID: 22
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RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE AV252Escherichia coliMutation(s): 0 
EC: 2.1.1.182
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1,542Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Other
  • Version 1.2: 2013-09-25
    Changes: Other
  • Version 1.3: 2017-08-23
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.4: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.5: 2018-04-11
    Changes: Data collection, Source and taxonomy