8K3O

Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli K-12
  • Mutation(s): No 

  • Deposited: 2023-07-16 Released: 2024-07-24 
  • Deposition Author(s): Afsar, M., Shukla, A., Ramachandran, R.
  • Funding Organization(s): Department of Science & Technology (DST, India), Council of Scientific & Industrial Research (CSIR), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Bacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism.

Afsar, M., Shukla, A., Ali, F., Maurya, R.K., Bharti, S., Kumar, N., Sadik, M., Chandra, S., Rahil, H., Kumar, S., Ansari, I., Jahan, F., Habib, S., Hussain, T., Krishnan, M.Y., Ramachandran, R.

(2024) Nucleic Acids Res 52: 13996-14012

  • DOI: https://doi.org/10.1093/nar/gkae1130
  • Primary Citation of Related Structures:  
    8K3O, 8K4E

  • PubMed Abstract: 

    Lesions and stable secondary structures in mRNA severely impact the translation efficiency, causing ribosome stalling and collisions. Prokaryotic ribosomal proteins Rps3, Rps4 and Rps5, located in the mRNA entry tunnel, form the mRNA helicase center and unwind stable mRNA secondary structures during translation. However, the mechanism underlying the detection of lesions on translating mRNA is unclear. We used Cryo-EM, biochemical assays, and knockdown experiments to investigate the apurinic/apyrimidinic (AP) endoribonuclease activity of bacterial ribosomes on AP-site containing mRNA. Our biochemical assays show that Rps3, specifically the 130RR131 motif, is important for recognizing and performing the AP-endoribonuclease activity. Furthermore, structural analysis revealed cleaved mRNA product in the 30S ribosome entry tunnel. Additionally, knockdown studies in Mycobacterium tuberculosis confirmed the protective role of Rps3 against oxidative and UV stress. Overall, our results show that prokaryotic Rps3 recognizes and processes AP-sites on mRNA via a novel mechanism that is distinct from eukaryotes.

    • Organizational Affiliation: 

    Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow-226031, India.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2A [auth B]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth C]233Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth D]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth E]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformE [auth F]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth G]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth H]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth I]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth J]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth K]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth L]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth M]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15M [auth O]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16N [auth P]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17O [auth Q]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18P [auth R]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Q [auth S]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20R [auth T]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21T [auth X]71Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14V [auth N]101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains LengthOrganismImage
Cleaved AP-mRNAS [auth V]24Escherichia coli K-12
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Entity ID: 21
MoleculeChains LengthOrganismImage
16S rRNAU [auth A]1,554Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Science & Technology (DST, India)IndiaGAP0292
Council of Scientific & Industrial Research (CSIR)IndiaCII7032 & MLP0107
Department of Biotechnology (DBT, India)IndiaGAP0384

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-01-08
    Changes: Data collection, Database references