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- PDB-6dzk: Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dzk | ||||||||||||
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Title | Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY | ||||||||||||
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![]() | RIBOSOME / Hibernation factor complex | ||||||||||||
Function / homology | ![]() negative regulation of translational elongation / ribosomal small subunit binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome ...negative regulation of translational elongation / ribosomal small subunit binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Sharma, M.R. / Li, Y. / Korripella, R. / Yang, Y. / Kaushal, P.S. / Lin, Q. / Wade, J.T. / Gray, A.G. / Derbyshire, K.M. / Agrawal, R.K. / Ojha, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Zinc depletion induces ribosome hibernation in mycobacteria. Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Yong Yang / Prem S Kaushal / Qishan Lin / Joseph T Wade / Todd A Gray / Keith M Derbyshire / Rajendra K Agrawal / Anil K Ojha / ![]() 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 ...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 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 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. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.2 KB | Display | ![]() |
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Full document | ![]() | 984.7 KB | Display | |
Data in XML | ![]() | 98.8 KB | Display | |
Data in CIF | ![]() | 166.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8934MC ![]() 8932C ![]() 8937C ![]() 6dziC ![]() 6dzpC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-30S ribosomal protein ... , 19 types, 19 molecules CDEFGHIJKLMOPQSTVrN
#3: Protein | Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7 |
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#4: Protein | Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7 |
#5: Protein | Mass: 21814.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG6 |
#6: Protein | Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS97 |
#8: Protein | Mass: 14361.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3 |
#9: Protein | Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9 |
#10: Protein | Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0 |
#11: Protein | Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6 |
#12: Protein | Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96 |
#13: Protein | Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL5 |
#14: Protein | Mass: 10236.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3 |
#15: Protein | Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37 |
#16: Protein | Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0 |
#17: Protein | Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5 |
#18: Protein | Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102 |
#19: Protein | Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVB8 |
#20: Protein | Mass: 9606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 11661.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R550 |
-Protein , 2 types, 2 molecules Yg
#21: Protein | Mass: 26447.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#23: Protein | Mass: 9141.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R554 |
-RNA chain / Protein/peptide , 2 types, 2 molecules AB
#1: RNA chain | Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
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#2: Protein/peptide | Mass: 4033.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QR10*PLUS |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mycobacterium smegmatis (Cminus) 70S with MPY / Type: RIBOSOME Details: Mycobacterium smegmatis 30S ribosomal subunit with MPY Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 67 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 205510 | |||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66840 / Symmetry type: POINT | |||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |