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 

wwPDB Validation   3D Report Full Report


This is version 1.7 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 ...

    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: 

    IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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Entity ID: 3
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30S ribosomal protein S3C233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 4
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30S ribosomal protein S4D206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 6
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30S ribosomal protein S6F131Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 7
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30S ribosomal protein S7G156Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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Entity ID: 8
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30S ribosomal protein S8H130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 9
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30S ribosomal protein S9I130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 10
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30S ribosomal protein S10J103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 11
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30S ribosomal protein S11K129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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Entity ID: 12
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30S ribosomal protein S12L123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 13
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30S ribosomal protein S13M118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 14
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30S ribosomal protein S14N101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Entity ID: 15
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30S ribosomal protein S15O89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 16
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30S ribosomal protein S16P102Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17Q84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 18
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30S ribosomal protein S18R75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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Entity ID: 19
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30S ribosomal protein S19S92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 20
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30S ribosomal protein S20T87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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Entity ID: 21
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30S ribosomal protein S21U71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-1V72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: infA, TTHA1669
UniProt
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Entity ID: 23
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Translation initiation factor IF-2W890Escherichia coli K-12Mutation(s): 0 
Gene Names: infB, gicD, ssyG, b3168, JW3137
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-3X [auth Y]171Geobacillus stearothermophilusMutation(s): 0 
Gene Names: infC
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Entity ID: 25
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Translation initiation factor IF-3Y [auth Z]144Escherichia coli K-12Mutation(s): 0 
Gene Names: infC, fit, srjA, b1718, JW5829
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1,534Escherichia coli K-12
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Entity ID: 26
MoleculeChainsLengthOrganismImage
fMet-tRNAZ [auth X]77Escherichia coli K-12
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Small Molecules
Ligands 1 Unique
IDChainsName / 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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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

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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