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- PDB-7bgd: Staphylococcus aureus 30S ribosomal subunit in presence of spermi... -

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Basic information

Entry
Database: PDB / ID: 7bgd
TitleStaphylococcus aureus 30S ribosomal subunit in presence of spermidine (body only)
Components
  • (30S ribosomal protein ...) x 12
  • 16S ribosomal RNA
  • mRNA
KeywordsRIBOSOME / Pathogen / small ribosomal subunit / spermidine
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex ...ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S6/Translation elongation factor EF1B / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily ...Ribosomal protein S6/Translation elongation factor EF1B / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / : / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S11 / Ribosomal protein S12 signature. / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBelinite, M. / Khusainov, I. / Marzi, S. / Romby, P. / Yusupov, M. / Hashem, Y.
Funding support France, 2items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-10-LABX-0036 NETRNA France
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0007-01 France
CitationJournal: Front Mol Biosci / Year: 2021
Title: Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in .
Authors: Margarita Belinite / Iskander Khusainov / Heddy Soufari / Stefano Marzi / Pascale Romby / Marat Yusupov / Yaser Hashem /
Abstract: Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution ...Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution structures using this approach, one needs to obtain homogeneous and stable samples, which requires optimization of ribosome purification in a species-dependent manner. This is especially critical for the bacterial small ribosomal subunit that tends to be unstable in the absence of ligands. Here, we report a protocol for purification of stable 30 S from the Gram-positive bacterium and its cryo-EM structures: in presence of spermidine at a resolution ranging between 3.4 and 3.6 Å and in its absence at 5.3 Å. Using biochemical characterization and cryo-EM, we demonstrate the importance of spermidine for stabilization of the 30 S preserving favorable conformation of the helix 44.
History
DepositionJan 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: mRNA
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
h: 30S ribosomal protein S8
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
t: 30S ribosomal protein S20


Theoretical massNumber of molelcules
Total (without water)688,72214
Polymers688,72214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55350 Å2
ΔGint-468 kcal/mol
Surface area194160 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules Aa

#1: RNA chain mRNA


Mass: 10392.300 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Production host: Escherichia coli (E. coli)
#2: RNA chain 16S ribosomal RNA


Mass: 503218.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: NCTC 8325

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30S ribosomal protein ... , 12 types, 12 molecules bdefhklopqrt

#3: Protein 30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ25
#4: Protein 30S ribosomal protein S4


Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXK6
#5: Protein 30S ribosomal protein S5


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW23
#6: Protein 30S ribosomal protein S6


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G113
#7: Protein 30S ribosomal protein S8


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW20
#8: Protein 30S ribosomal protein S11


Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW31
#9: Protein 30S ribosomal protein S12


Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0H0
#10: Protein 30S ribosomal protein S15


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G2Q1
#11: Protein 30S ribosomal protein S16


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ45
#12: Protein 30S ribosomal protein S17


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW15
#13: Protein 30S ribosomal protein S18


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G111
#14: Protein 30S ribosomal protein S20


Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXY6

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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

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus aureus 30S ribosomal subunit in the presence of spermidine (body only)RIBOSOMEall0MULTIPLE SOURCES
230S ribosomal subunitCOMPLEX#2-#141NATURAL
3mRNACOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)93061
33Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)93061
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: Gctf / Version: 1.06 / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529602 / Symmetry type: POINT

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