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Yorodumi- PDB-6dzi: Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dzi | ||||||||||||
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Title | Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex | ||||||||||||
Components |
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Keywords | RIBOSOME / Hibernation factor complex | ||||||||||||
Function / homology | Function and homology information negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) Mycobacterium smegmatis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | ||||||||||||
Authors | 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 | United States, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dzi.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6dzi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6dzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dzi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6dzi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6dzi_validation.xml.gz | 213.9 KB | Display | |
Data in CIF | 6dzi_validation.cif.gz | 385.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/6dzi ftp://data.pdbj.org/pub/pdb/validation_reports/dz/6dzi | HTTPS FTP |
-Related structure data
Related structure data | 8932MC 8934C 8937C 6dzkC 6dzpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.2210/pdb5O61/pdb / Data set type: other data / Metadata reference: 10.1016/j.celrep.2017.06.029 |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules hAB
#1: RNA chain | Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16 S RNA Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
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#23: RNA chain | Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
#24: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
-Protein/peptide , 2 types, 2 molecules j3
#2: Protein/peptide | Mass: 4033.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 |
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#56: Protein/peptide | Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTP4 |
-30S ribosomal protein ... , 19 types, 19 molecules klmnpq4stuvxz5678r9
#3: Protein | Mass: 23617.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7 |
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#4: Protein | Mass: 23284.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7 |
#5: Protein | Mass: 18481.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) 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) Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0D6J3X3 |
#7: Protein | Mass: 17529.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) 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) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3 |
#9: Protein | Mass: 14093.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9 |
#10: Protein | Mass: 11252.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0 |
#11: Protein | Mass: 12151.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6 |
#12: Protein | Mass: 13678.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96 |
#13: Protein | Mass: 13374.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) 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) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3 |
#15: Protein | Mass: 12635.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37 |
#16: Protein | Mass: 10680.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0 |
#17: Protein | Mass: 9379.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5 |
#18: Protein | Mass: 9424.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102 |
#19: Protein | Mass: 25576.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVB8 |
#20: Protein | Mass: 9449.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R549 |
#22: Protein | Mass: 11661.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R550 |
-Protein , 1 types, 1 molecules Y
#21: Protein | Mass: 12238.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTK6 |
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+50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXZabcdefgy
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 70S-MPY complex / Type: RIBOSOME Details: Mycobacterium smegmatis ribosome (Cminus) 70S-MPY complex Entity ID: #1-#53, #55-#56 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 67.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66840 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |