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- PDB-8whx: Cryo- EM structure of Mycobacterium smegmatis 70S ribosome and RafH. -
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Open data
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Basic information
Entry | Database: PDB / ID: 8whx | ||||||
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Title | Cryo- EM structure of Mycobacterium smegmatis 70S ribosome and RafH. | ||||||
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Function / homology | ![]() negative regulation of translational elongation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, N. / Sharma, S. / Kaushal, P.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Authors: Niraj Kumar / Shivani Sharma / Prem S Kaushal / ![]() 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 ...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), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF 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 NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF 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 structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.5 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37551MC ![]() 8whyC ![]() 8wi7C ![]() 8wi8C ![]() 8wi9C ![]() 8wibC ![]() 8wicC ![]() 8widC ![]() 8wifC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+50S ribosomal protein ... , 26 types, 26 molecules EFGHIJMNOQRSTUVWXZ12356784
-RNA chain , 3 types, 3 molecules ABa
#27: RNA chain | ![]() Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 |
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#28: RNA chain | ![]() Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: GenBank: 118168627 |
#29: RNA chain | ![]() Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: GenBank: 118168627 |
-30S ribosomal protein ... , 20 types, 20 molecules vdefghijklmnopqrstuc
#30: Protein/peptide | ![]() Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QR10 |
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#31: Protein | ![]() Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSD7 |
#32: Protein | ![]() Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSL7 |
#33: Protein | ![]() Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSG6 |
#34: Protein | ![]() Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0A8B4QKV6 |
#35: Protein | ![]() Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QS97 |
#36: Protein | ![]() Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSG3 |
#37: Protein | ![]() Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSP9 |
#38: Protein | ![]() Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSD0 |
#39: Protein | ![]() Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSL6 |
#40: Protein | ![]() Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QS96 |
#41: Protein | ![]() Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSL5 |
#42: Protein | ![]() Mass: 11792.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0R550 |
#43: Protein | ![]() Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QVQ3 |
#44: Protein | ![]() Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QV37 |
#45: Protein | ![]() Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSE0 |
#46: Protein | ![]() Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0R7F7 |
#47: Protein | ![]() Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QSD5 |
#48: Protein | ![]() Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0R102 |
#49: Protein | ![]() Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: mc(2)155 / References: UniProt: A0QVB8 |
-Protein , 1 types, 1 molecules w
#50: Protein | Mass: 29898.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: mc(2)155 / Gene: MSMEG_3935 / Production host: ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 20mM HEPES, 20mM MgCl2, 100mM NH4Cl, 3mM DTT | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / 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![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 1.34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 12343 |
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Processing
EM software |
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CTF correction![]() | Details: CTF correction in Relion / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1202461 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110934 / Num. of class averages: 3 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: phenix.real_space_refinement | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6DZI Accession code: 6DZI / Source name: PDB / Type: experimental model |