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- PDB-7kwg: Staphylococcus aureus 30S ribosomal subunit in presence of spermidine -

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Basic information

Entry
Database: PDB / ID: 7kwg
TitleStaphylococcus aureus 30S ribosomal subunit in presence of spermidine
Components
  • (30S ribosomal protein ...) x 19
  • 16S ribosomal RNA
  • mRNA
KeywordsRIBOSOME / Pathogen / small ribosomal subunit / spermidine
Function / homology
Function and homology information


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 ...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 / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 ...Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S2 signature 2. / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / : / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / 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 / Small ribosomal subunit protein uS10
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 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
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: mRNA
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14 type Z
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20


Theoretical massNumber of molelcules
Total (without water)788,85421
Polymers788,85421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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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 subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / 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 subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381

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30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst

#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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FZ25
#4: Protein 30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW12
#5: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FXK6
#6: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW23
#7: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G113
#8: Protein 30S ribosomal protein S7


Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: P48940
#9: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW20
#10: Protein 30S ribosomal protein S9


Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW39
#11: Protein 30S ribosomal protein S10


Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: A0A380EDM5, UniProt: Q931G5*PLUS
#12: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW31
#13: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: P0A0H0
#14: Protein 30S ribosomal protein S13


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW30
#15: Protein 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW19
#16: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G2Q1
#17: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FZ45
#18: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW15
#19: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G111
#20: Protein 30S ribosomal protein S19


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW10
#21: 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 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / 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

ComponentName: Staphylococcus aureus 30S ribosomal subunit in presence of spermidine
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
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: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529602 / Symmetry type: POINT

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