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- PDB-8wid: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wid | ||||||
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Title | Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, E- tRNA and RafH. | ||||||
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![]() | RIBOSOME / protein synthesis / Mycobacterium smegmatis / hibernation promotion factor / HPF / RafH / hypoxia stress / Cryo- EM / Single particle reconstruction | ||||||
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 / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 890.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37564MC ![]() 8whxC ![]() 8whyC ![]() 8wi7C ![]() 8wi8C ![]() 8wi9C ![]() 8wibC ![]() 8wicC ![]() 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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Components
-RNA chain , 2 types, 2 molecules ab
#1: RNA chain | Mass: 491662.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
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#2: RNA chain | Mass: 24465.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
-30S ribosomal protein ... , 19 types, 19 molecules vdefghijklmnopqrstu
#3: Protein/peptide | Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QR10 |
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#4: Protein | Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSD7 |
#5: Protein | Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL7 |
#6: Protein | Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSG6 |
#7: Protein | Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A8B4QKV6 |
#8: Protein | Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QS97 |
#9: Protein | Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSG3 |
#10: Protein | Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSP9 |
#11: Protein | Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSD0 |
#12: Protein | Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL6 |
#13: Protein | Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QS96 |
#14: Protein | Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSL5 |
#15: Protein | Mass: 11792.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R550 |
#16: Protein | Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QVQ3 |
#17: Protein | Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QV37 |
#18: Protein | Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSE0 |
#19: Protein | Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R7F7 |
#20: Protein | Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0QSD5 |
#21: Protein | Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R102 |
-Protein , 2 types, 2 molecules xw
#22: Protein | Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0R215 |
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#23: Protein | Mass: 29898.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MSMEG_3935 / Production host: ![]() ![]() |
-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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 20mM HEPES, 100mM NH4Cl, 20mM MgCl2, 3mM DTT, | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
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 / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm |
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 Relion3.1.4 / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 44299 / Details: Ad-hoc low pass filter, 3.5 Angstrom / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8WHX Accession code: 8WHX / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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