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 1.4 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:  
    1X18, 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. We have obtained a three-dimensional cryo-electron microscopic map of the Thermus thermophilus 30S-Era complex ...

    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: 
    • 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: a GTPase-dependent cell cycle regulator containing an RNA binding motif
      Chen, X., Court, D.L., Ji, X.
      (1999) Proc Natl Acad Sci U S A 96: 8396
    • 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

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2E231Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  P80371
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80371
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7F154Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP17291
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11G119Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP80376
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18H73Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SLQ0
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding protein eraI [auth X]292Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3'A 11Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (31-MER)B 31Thermus thermophilus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(P*UP*UP*CP*CP*CP*GP*GP*GP*CP*CP*UP*GP*GP*GP*GP*CP*CP*CP*GP*C)-3'C 20Thermus thermophilus
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Entity ID: 4
MoleculeChainsLengthOrganismImage
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'D 24Thermus thermophilus
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Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-12-18
    Changes: Structure summary
  • Version 1.4: 2019-12-18
    Changes: Data collection, Database references