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- PDB-5zet: M. smegmatis P/P state 50S ribosomal subunit -

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Entry
Database: PDB / ID: 5zet
TitleM. smegmatis P/P state 50S ribosomal subunit
Components
  • (50S ribosomal protein ...) x 31
  • 23S rRNA23S ribosomal RNA
  • P-tRNAfMet
  • Uncharacterized protein bL37
KeywordsRIBOSOME / translating-state / complex
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / metal ion binding
Similarity search - Function
Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 ...Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L25, beta domain / Ribosomal protein L10 / Rubrerythrin, domain 2 / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L11, bacterial-type / RRM (RNA recognition motif) domain / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L10P / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11/L12 / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Single Sheet / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Similarity search - Domain/homology
RNA (> 1000) / 50S ribosomal protein L27 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / Uncharacterized protein / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L21 ...RNA (> 1000) / 50S ribosomal protein L27 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / Uncharacterized protein / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L21 / 50S ribosomal protein L15 / 50S ribosomal protein L31 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 50S ribosomal protein L34 / 50S ribosomal protein L18 / 50S ribosomal protein L28 / 50S ribosomal protein L36 / 50S ribosomal protein L18 / 50S ribosomal protein L30 / 50S ribosomal protein L4 / RNA (> 10) / RNA / : / 50S ribosomal protein L33 1 / 50S ribosomal protein L11 / 50S ribosomal protein L10 / 50S ribosomal protein L3 / 50S ribosomal protein L23 / RNA (> 100) / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L25
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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

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Structure visualization

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Assembly

Deposited unit
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
B: P-tRNAfMet
A: 23S rRNA
1: 50S ribosomal protein L30
2: 50S ribosomal protein L31
3: 50S ribosomal protein L32
4: 50S ribosomal protein L33 1
5: 50S ribosomal protein L34
6: 50S ribosomal protein L35
7: 50S ribosomal protein L36
8: Uncharacterized protein bL37


Theoretical massNumber of molelcules
Total (without water)1,485,56134
Polymers1,485,56134
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area168240 Å2
ΔGint-1402 kcal/mol
Surface area528070 Å2

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Components

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234567

#1: Protein 50S ribosomal protein L2 / / uL2


Mass: 30425.945 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: UniProt: A0QSD4
#2: Protein 50S ribosomal protein L3 / / uL3


Mass: 23011.393 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: UniProt: A0QSD1
#3: Protein 50S ribosomal protein L4 / / uL4


Mass: 22920.949 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: UniProt: A0QSD2
#4: Protein 50S ribosomal protein L5 / / uL5


Mass: 21152.328 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: UniProt: A0QSG1
#5: Protein 50S ribosomal protein L6 / / uL6


Mass: 19483.361 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: UniProt: A0QSG4
#6: Protein 50S ribosomal protein L9 / / bL9


Mass: 15949.253 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: UniProt: A0R7F6
#7: Protein 50S ribosomal protein L10 / / uL10


Mass: 18035.736 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: UniProt: A0QS62
#8: Protein 50S ribosomal protein L11 / / uL11


Mass: 15023.374 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: UniProt: A0QS45
#9: Protein 50S ribosomal protein L13 / / uL13


Mass: 16146.689 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: UniProt: A0QSP8
#10: Protein 50S ribosomal protein L14 / / uL14


Mass: 13400.625 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: UniProt: A0QSF9
#11: Protein 50S ribosomal protein L15 / / uL15


Mass: 15602.244 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: UniProt: A0QSG8
#12: Protein 50S ribosomal protein L16 / / uL16


Mass: 15774.240 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: UniProt: A0QSD8
#13: Protein 50S ribosomal protein L17 / / bL17


Mass: 21892.246 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: UniProt: A0QSL9
#14: Protein 50S ribosomal protein L18 / / uL18


Mass: 13711.728 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: UniProt: I7FGD9, UniProt: A0QSG5*PLUS
#15: Protein 50S ribosomal protein L19 / / bL19


Mass: 12892.806 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: UniProt: A0QV42
#16: Protein 50S ribosomal protein L20 / / bL20


Mass: 14494.693 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: UniProt: A0QYU6
#17: Protein 50S ribosomal protein L21 / / bL21


Mass: 11055.894 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: UniProt: A0R151
#18: Protein 50S ribosomal protein L22 / / uL22


Mass: 16353.600 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: UniProt: A0QSD6
#19: Protein 50S ribosomal protein L23 / / uL23


Mass: 11047.836 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: UniProt: A0QSD3
#20: Protein 50S ribosomal protein L24 / / uL24


Mass: 11228.946 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: UniProt: A0QSG0
#21: Protein 50S ribosomal protein L25 / / bL25 / General stress protein CTC


Mass: 22571.078 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: UniProt: I7GFB2, UniProt: A0R3D2*PLUS
#22: Protein 50S ribosomal protein L27 / / bL27


Mass: 9249.582 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: UniProt: A0R150
#23: Protein 50S ribosomal protein L28 / / bL28


Mass: 6891.016 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: UniProt: I7FJ52, UniProt: A0QV03*PLUS
#24: Protein 50S ribosomal protein L29 / / uL29


Mass: 8790.895 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: UniProt: A0QSD9
#27: Protein 50S ribosomal protein L30 / / uL30


Mass: 7022.147 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: UniProt: A0QSG7
#28: Protein 50S ribosomal protein L31 / / bL31


Mass: 8312.485 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: UniProt: A0R215
#29: Protein 50S ribosomal protein L32 / / bL32


Mass: 6467.719 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: UniProt: A0R3I9
#30: Protein 50S ribosomal protein L33 1 / Ribosome / bL33


Mass: 6468.501 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: UniProt: A0QS39
#31: Protein/peptide 50S ribosomal protein L34 / / bL34


Mass: 5522.580 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: UniProt: A0R7K0
#32: Protein 50S ribosomal protein L35 / / bL35


Mass: 7298.505 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: UniProt: A0QYU7
#33: Protein/peptide 50S ribosomal protein L36 / / bL36


Mass: 4341.277 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: UniProt: A0QSL4

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RNA chain , 2 types, 2 molecules BA

#25: RNA chain P-tRNAfMet


Mass: 38038.777 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
#26: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 1012140.938 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

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Protein/peptide , 1 types, 1 molecules 8

#34: Protein/peptide Uncharacterized protein bL37


Mass: 2841.375 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: UniProt: A0QTP4

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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: Translating-state 50S ribosome structure from M.smegmatis
Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL
Molecular weightExperimental 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 391837 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å

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