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- PDB-5zey: M. smegmatis Trans-translation state 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 5zey
TitleM. smegmatis Trans-translation state 70S ribosome
Components
  • A-tRNAfMet
  • SsrA-binding protein
  • tmRNATransfer-messenger RNA
KeywordsRNA BINDING PROTEIN/RNA / trans-translating state / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


trans-translation / RNA binding / cytoplasm
Similarity search - Function
SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein.
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / SsrA-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsMishra, S. / Ahmed, T. / Tyagi, A. / Shi, J. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: Sci Rep / Year: 2018
Title: Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.
Authors: Satabdi Mishra / Tofayel Ahmed / Anu Tyagi / Jian Shi / Shashi Bhushan /
Abstract: Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these ...Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.
History
DepositionFeb 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource / struct_keywords
Item: _em_entity_assembly.type / _em_entity_assembly_naturalsource.id ..._em_entity_assembly.type / _em_entity_assembly_naturalsource.id / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: tmRNA
B: A-tRNAfMet
C: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)162,3203
Polymers162,3203
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area92270 Å2

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Components

#1: RNA chain tmRNA / Transfer-messenger RNA


Mass: 119208.492 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: GenBank: 118168627
#2: RNA chain A-tRNAfMet


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1036415628
#3: Protein SsrA-binding protein / Small protein B


Mass: 18325.039 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: A0QU63

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tmRNA and SmpB in trans-translating state of M. smegmatis
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Cellular location: cytoplasm
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 391837 / Symmetry type: POINT

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