Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - ABCDE 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126115.64 
• Atom Count: 955 
• Residue Count: 955 
• Unique protein chains: 5
• Unique nucleic acid chains: 4

1X18

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

• DOI: 10.2210/pdb1X18/pdb

• Classification: STRUCTURAL PROTEIN/RNA
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2005-04-02 Released: 2005-05-17 
• Deposition Author(s): Sharma, M.R., Barat, C., Agrawal, R.K.

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Experimental Data Snapshot

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

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

• PubMed: 15866174 
• 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. 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.

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Related Citations: 

• 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 --: --
• 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




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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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	E	231	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80371

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	F	154	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P17291

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	G	119	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80376

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	H	73	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLQ0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
GTP-binding protein era	X	292	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(P*CP*GP*AP*UP*GP*GP*CP*GP*AP*AP*G)-3'	A	11	Thermus thermophilus

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (31-MER)	B	31	Thermus thermophilus

Entity ID: 3
Molecule	Chains	Length	Organism
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	20	Thermus thermophilus

Entity ID: 4
Molecule	Chains	Length	Organism
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	24	Thermus thermophilus

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-02 
• Released Date: 2005-05-17 
• Deposition Author(s): Sharma, M.R., Barat, C., Agrawal, R.K.

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