2R1G

Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural aspects of RbfA action during small ribosomal subunit assembly.

Datta, P.P.Wilson, D.N.Kawazoe, M.Swami, N.K.Kaminishi, T.Sharma, M.R.Booth, T.M.Takemoto, C.Fucini, P.Yokoyama, S.Agrawal, R.K.

(2007) Mol.Cell 28: 434-445

  • DOI: 10.1016/j.molcel.2007.08.026
  • Primary Citation of Related Structures:  2DYJ, 2R1C

  • PubMed Abstract: 
  • Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure ...

    Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.


    Related Citations: 
    • Structure of the 30S ribosomal subunit
      Wimberly, B.T.,Brodersen, D.E.,Clemons, W.M.,Morgan-Warren, R.J.,Carter, A.P.,Vonrhein, C.,Hartsch, T.,Ramakrishnan, V.
      (2000) Nature 407: 327


    Organizational Affiliation

    Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
G
127Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
H
124Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
I
125Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 1
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 1A24N/A
Entity ID: 2
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 18B48N/A
Entity ID: 3
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 27C29N/A
Entity ID: 4
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 28D28N/A
Entity ID: 5
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 44E11N/A
Entity ID: 6
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 44X11N/A
Entity ID: 7
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNA HELIX 45F29N/A
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance