5ME0

Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112


Experimental Data Snapshot

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

Starting Models: experimental
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This is version 1.8 of the entry. See complete history


Literature

Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.

Lopez-Alonso, J.P.Fabbretti, A.Kaminishi, T.Iturrioz, I.Brandi, L.Gil-Carton, D.Gualerzi, C.O.Fucini, P.Connell, S.R.

(2017) Nucleic Acids Res 45: 2179-2187

  • DOI: https://doi.org/10.1093/nar/gkw1251
  • Primary Citation of Related Structures:  
    5ME0, 5ME1

  • PubMed Abstract: 

    In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.


  • Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6131Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7156Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1784Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-172Thermus thermophilus HB8Mutation(s): 0 
Gene Names: infATTHA1669
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2890Escherichia coli K-12Mutation(s): 0 
Gene Names: infBgicDssyGb3168JW3137
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3X [auth Y]171Geobacillus stearothermophilusMutation(s): 0 
Gene Names: infC
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3Y [auth Z]144Escherichia coli K-12Mutation(s): 0 
Gene Names: infCfitsrjAb1718JW5829
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,534Escherichia coli K-12
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Entity ID: 26
MoleculeChains LengthOrganismImage
fMet-tRNAZ [auth X]77Escherichia coli K-12
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
AA [auth X]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTCoot0.8.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionItalyQLRT- 2001-00892
Marie Curie Actions; COFUNDSpain--
Marie Curie Action Career Integration GrantSpainPCIG14-GA-2013-632072
Spanish Ministry of Economy and CompetitivenessSpainCTQ2014-55907-R

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2019-10-23
    Changes: Data collection, Other
  • Version 1.7: 2019-11-13
    Changes: Data collection, Other
  • Version 1.8: 2024-04-24
    Changes: Data collection, Database references, Derived calculations, Refinement description