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- PDB-6sj6: Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6sj6
TitleCryo-EM structure of 50S-RsfS complex from Staphylococcus aureus
Components
  • (50S ribosomal protein ...) x 23
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosomal silencing factor RsfS
KeywordsRIBOSOME / Stress / S.aureus / RsfS / Hibernation
Function / homology
Function and homology information


negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 ...Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L22/L17 / Ribosomal Protein L30; Chain: A, / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / RRM (RNA recognition motif) domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L2 signature. / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribosomal protein L2, conserved site / : / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Ribosomal silencing factor RsfS
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsKhusainov, I. / Pellegrino, S. / Yusupova, G. / Yusupov, M. / Fatkhullin, B.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0021-01 France
French National Research AgencyANR-16-CE11-0007-01 France
French National Research AgencyLabex: ANR-10-LABX- 0036_NETRNA France
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.
Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A ...Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A Sprenger / Shamil Validov / Konstantin Usachev / Gulnara Yusupova / Marat Yusupov /
Abstract: For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced ...For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced proteins to the ribosome to prevent unnecessary translation. One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. The understanding of the detailed landscape of RsfS-uL14 interactions within the ribosome shed light on the mechanism of ribosome shutdown in the human pathogen S. aureus and might deliver a novel target for pharmacological drug development and treatment of bacterial infections.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: 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
Revision 1.2Jul 8, 2020Group: Structure summary / Category: audit_author
Revision 1.3May 22, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Y: 50S ribosomal protein L25
Z: 50S ribosomal protein L27
0: 50S ribosomal protein L28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
4: 50S ribosomal protein L32
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
9: Ribosomal silencing factor RsfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,312,59485
Polymers1,311,11626
Non-polymers1,47859
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area131840 Å2
ΔGint-1589 kcal/mol
Surface area464230 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 23S ribosomal RNA


Mass: 946696.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: GenBank: 1613890206
#2: RNA chain 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: GenBank: 1569642733

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50S ribosomal protein ... , 23 types, 23 molecules DEFMNOPQRSTUVWXYZ012467

#3: Protein 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: P60430
#4: Protein 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW06
#5: Protein 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW07
#6: Protein 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW38
#7: Protein 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW16
#8: Protein 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: P0A0F8
#9: Protein 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW13
#10: Protein 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW33
#11: Protein 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW22
#12: Protein 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ42
#13: Protein 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXQ1
#14: Protein 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXS8
#15: Protein 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW11
#16: Protein 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW08
#17: Protein 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW17
#18: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2G0S0
#19: Protein 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXT0
#20: Protein 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ60
#21: Protein 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW14
#22: Protein 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: P0A0G2
#23: Protein 50S ribosomal protein L32


Mass: 6657.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZF1
#24: Protein/peptide 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FUQ0
#25: Protein 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXQ0

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Protein , 1 types, 1 molecules 9

#26: Protein Ribosomal silencing factor RsfS


Mass: 13497.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: rsfS, SAOUHSC_01695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G298

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Non-polymers , 2 types, 59 molecules

#27: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: Mg
#28: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN

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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
150S ribosomal subunit complex with stress induced ribosome silencing factor RsfS from Staphylococcus aureusRIBOSOME#1-#260MULTIPLE SOURCES
250S ribosomal subunitORGANELLE OR CELLULAR COMPONENT#1-#251NATURAL
3Ribosomal silencing factor RsfSCOMPLEX#261RECOMBINANT
Molecular weightValue: 1.35 MDa / Experimental value: YES
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 BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepesC8H18N2O4S1
250 mMpotassium chlorideKCl1
310 mMammonium chlorideNH4Cl1
410 mMmagnesium acetateMg(CH3OO)21
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 43 sec. / Electron dose: 24.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1856

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4GctfCTF correction
7MDFFmodel fittingflexible fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
19PHENIXmodel refinementfirst refinement
20Cootmodel refinementmanual correction
21PHENIXmodel refinementfinal minimization
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 172729
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83885 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5LI0

5li0


Accession code: 5LI0 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008134817
ELECTRON MICROSCOPYf_angle_d0.996241354
ELECTRON MICROSCOPYf_dihedral_angle_d26.74753446
ELECTRON MICROSCOPYf_chiral_restr0.05416590
ELECTRON MICROSCOPYf_plane_restr0.00510769

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