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- PDB-6wub: 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBod... -

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Basic information

Entry
Database: PDB / ID: 6wub
Title30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Components
  • (30S ribosomal protein ...) x 11
  • 16S rRNA
KeywordsRIBOSOME / 70S / pathogen / antibiotic development / antibiotic resistant
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 / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm / cytosol
Similarity search - Function
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 S18, conserved site / Ribosomal protein S18 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 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 S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / 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 S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / 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 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. / Ribosomal protein S11 / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEnterococcus faecalis OG1RF (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJogl, G. / Khayat, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)G12MD007603 United States
CitationJournal: Sci Rep / Year: 2020
Title: Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
Authors: Eileen L Murphy / Kavindra V Singh / Bryant Avila / Torsten Kleffmann / Steven T Gregory / Barbara E Murray / Kurt L Krause / Reza Khayat / Gerwald Jogl /
Abstract: Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ...Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / 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
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

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Structure visualization

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  • EMDB-21909
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Assembly

Deposited unit
a: 16S rRNA
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)641,78012
Polymers641,78012
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 , 1 types, 1 molecules a

#1: RNA chain 16S rRNA


Mass: 501090.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: GenBank: 327533853

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30S ribosomal protein ... , 11 types, 11 molecules defhklopqrt

#2: Protein 30S ribosomal protein S4


Mass: 23029.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRV7, UniProt: Q82ZI6*PLUS
#3: Protein 30S ribosomal protein S5


Mass: 17156.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKW0, UniProt: Q839E7*PLUS
#4: Protein 30S ribosomal protein S6


Mass: 11331.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB6, UniProt: Q839Z0*PLUS
#5: Protein 30S ribosomal protein S8


Mass: 14805.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS6, UniProt: Q839F0*PLUS
#6: Protein 30S ribosomal protein S11


Mass: 12322.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKV1, UniProt: Q839E0*PLUS
#7: Protein 30S ribosomal protein S12


Mass: 15178.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKQ7, UniProt: Q839H1*PLUS
#8: Protein 30S ribosomal protein S15


Mass: 10537.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XRW3, UniProt: Q82ZJ1*PLUS
#9: Protein 30S ribosomal protein S16


Mass: 10095.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XP69, UniProt: Q834F9*PLUS
#10: Protein 30S ribosomal protein S17


Mass: 9744.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKS3, UniProt: Q839F5*PLUS
#11: Protein 30S ribosomal protein S18


Mass: 7646.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XKB3, UniProt: Q839Y8*PLUS
#12: Protein 30S ribosomal protein S20


Mass: 8841.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis OG1RF (bacteria) / References: UniProt: A0A1B4XQJ7, UniProt: Q831Q7*PLUS

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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: Enterococcus faecalis / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K / Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec

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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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.14_3235model refinement
10RELION3.1initial Euler assignment
11cryoSPARC0.63final Euler assignment
12FREALIGN9.03classification
13cryoSPARC0.633D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335675 / Symmetry type: POINT
Atomic model buildingB value: 177 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15LI0

5li0

15LI01PDBexperimental model
24YBB

4ybb

14YBB2PDBexperimental model

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