6DZP

Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Zinc depletion induces ribosome hibernation in mycobacteria.

Li, Y.Sharma, M.R.Koripella, R.K.Yang, Y.Kaushal, P.S.Lin, Q.Wade, J.T.Gray, T.A.Derbyshire, K.M.Agrawal, R.K.Ojha, A.K.

(2018) Proc Natl Acad Sci U S A 115: 8191-8196

  • DOI: https://doi.org/10.1073/pnas.1804555115
  • Primary Citation of Related Structures:  
    6DZI, 6DZK, 6DZP

  • PubMed Abstract: 

    Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in Mycobacterium smegmatis is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in Mycobacterium tuberculosis in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB.


  • Organizational Affiliation

    Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5186Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13146Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18126Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I7FGD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21102Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22152Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2399Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2788Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth a]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth b]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 2BA [auth c]54Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R551 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth d]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth e]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31FA [auth g]82Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28GA [auth y]78Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinHA [auth 3]23Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA3,119Mycolicibacterium smegmatis MC2 155
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA118Mycolicibacterium smegmatis MC2 155
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM061576
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI107595
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI097191

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references