1X18

Contact sites of ERA GTPase on the THERMUS THERMOPHILUS 30S SUBUNIT


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interaction of Era with the 30S Ribosomal Subunit Implications for 30S Subunit Assembly

Sharma, M.R.Barat, C.Wilson, D.N.Booth, T.M.Kawazoe, M.Hori-Takemoto, C.Shirouzu, M.Yokoyama, S.Fucini, P.Agrawal, R.K.

(2005) Mol.Cell 18: 319-329

  • DOI: 10.1016/j.molcel.2005.03.028
  • Primary Citation of Related Structures:  1X1L

  • PubMed Abstract: 
  • Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to accumulation of an unprocessed precursor of the 16S rRNA. ...

    Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to accumulation of an unprocessed precursor of the 16S rRNA. We have obtained a three-dimensional cryo-electron microscopic map of the Thermus thermophilus 30S-Era complex. Era binds in the cleft between the head and platform of the 30S subunit and locks the subunit in a conformation that is not favorable for association with the large (50S) ribosomal subunit. The RNA binding KH motif present within the C-terminal domain of Era interacts with the conserved nucleotides in the 3' region of the 16S rRNA. Furthermore, Era makes contact with several assembly elements of the 30S subunit. These observations suggest a direct involvement of Era in the assembly and maturation of the 30S subunit.


    Related Citations: 
    • Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif
      Chen, X.,Court, D.L.,Ji, X.
      (1999) Proc.Natl.Acad.Sci.USA 96: 8396
    • Structure of the 30S ribosomal subunit
      Wimberly, B.T.,Brodersen, D.E.,Clemons Jr., W.M.,Morgan-Warren, R.J.,Carter, A.P.,Vonrhein, C.,Hartsch, T.,Ramakrishnan, V.
      (2000) Nature 407: 327
    • Crystal structure of Era from Thermus thermophilus
      Kawazoe, M.,Takemoto, C.,Kaminishi, T.,Sekine, S.,Shirouzu, M.,Fucini, P.,Agrawal, R.K.,Yokoyama, S.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
E
231Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
F
154Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
G
119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
H
73Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein era
X
292N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3'A11Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (31-MER)B31Thermus thermophilus
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(P*UP*UP*CP*CP*CP*GP*GP*GP*CP*CP*UP*GP*GP*GP*GP*CP*CP*CP*GP*C)-3'C20Thermus thermophilus
Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(P*UP*GP*UP*UP*GP*GP*GP*UP*UP*AP*AP*GP*UP*CP*CP*CP*GP*CP*AP*AP*CP*GP*AP*G)-3'D24Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 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: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-12-18
    Type: Structure summary