6DZK

Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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: 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 ...

    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

    Department of Biomedical Sciences, University at Albany, Albany, NY 12208.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved domain protein B32Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0945
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 C275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 D201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 E213Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 F96Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: rpsFERS451418_06682
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 G156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 H131Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 I150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 J101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 K138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 L124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 M124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 O88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 P156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 Q98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 S93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 T86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 V277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 1 r85Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsR1rpsR2MSMEG_6065MSMEI_5905
Find proteins for A0R549 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promoting factor Y230Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: hpfMSMEG_1878
Find proteins for A0QTK6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 N100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsNMSMEG_6066MSMEI_5906
Find proteins for A0R550 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 g82Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_6070
Find proteins for A0R554 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1511Mycolicibacterium smegmatis MC2 155
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence