6W7N

30S-Inactive-low-Mg2+ Class A

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history. 


Literature

Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.

Jahagirdar, D., Jha, V., Basu, K., Gomez-Blanco, J., Vargas, J., Ortega, J.

(2020) RNA 26: 2017-2030

  • DOI: https://doi.org/10.1261/rna.075846.120
  • Primary Citation of Related Structures:  
    6W6K, 6W77, 6W7M, 6W7N, 6W7W

  • PubMed Abstract: 

    • It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation ...

    It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.

    Organizational Affiliation: 

    Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth C]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Entity ID: 3
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30S ribosomal protein S4C [auth D]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 4
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30S ribosomal protein S5D [auth E]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 5
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30S ribosomal protein S8E [auth H]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 6
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30S ribosomal protein S9F [auth I]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 7
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30S ribosomal protein S10G [auth J]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 8
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30S ribosomal protein S12H [auth L]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 9
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30S ribosomal protein S13I [auth M]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 10
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30S ribosomal protein S14J [auth N]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 11
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30S ribosomal protein S15K [auth O]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16L [auth P]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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Entity ID: 13
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30S ribosomal protein S17M [auth Q]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 14
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30S ribosomal protein S19N [auth S]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 15
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30S ribosomal protein S20O [auth T]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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Entity ID: 1
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16S rRNA1,542Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaCIHR PJT- 153044

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references