8WIC

Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, E- tRNA and RafH.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.

Kumar, N.Sharma, S.Kaushal, P.S.

(2024) Nat Commun 15: 638-638

  • DOI: https://doi.org/10.1038/s41467-024-44879-y
  • Primary Citation of Related Structures:  
    8WHX, 8WHY, 8WI7, 8WI8, 8WI9, 8WIB, 8WIC, 8WID, 8WIF

  • PubMed Abstract: 

    Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF long ), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF long induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF long NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF long CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF long structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.


  • Organizational Affiliation

    Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth E]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth F]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth G]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth H]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth I]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9F [auth J]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth N]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth O]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth Q]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth R]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth S]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20M [auth T]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth U]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22O [auth V]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P [auth W]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth X]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27R [auth Z]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28S [auth 1]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29T [auth 2]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30U [auth 3]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth 5]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AW [auth 6]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth 7]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35Y [auth 8]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [auth 4]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains LengthOrganismImage
23S rRNAAA [auth A]3,119Mycolicibacterium smegmatis MC2 155
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S rRNABA [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 29
MoleculeChains LengthOrganismImage
E-tRNACA [auth C]76Mycolicibacterium smegmatis MC2 155
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)India--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release