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- PDB-8cvo: Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound,... -

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Basic information

Entry
Database: PDB / ID: 8cvo
TitleCutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Components
  • (30S ribosomal protein ...) x 8
  • 16S ribosomal RNA
KeywordsANTIBIOTIC / ribosome / sarecycline / acne
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / K Homology domain / K homology RNA-binding domain ...Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Sarecycline / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S10 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S3 / 30S ribosomal protein S19 ...Sarecycline / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S10 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S3 / 30S ribosomal protein S19 / 30S ribosomal protein S7 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S9 / 30S ribosomal protein S13
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsLomakin, I.B. / Devarkar, S.C. / Bunick, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Almirall, LLC United States
Citation
Journal: Nucleic Acids Res / Year: 2023
Title: Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.
Authors: Ivan B Lomakin / Swapnil C Devarkar / Shivali Patel / Ayman Grada / Christopher G Bunick /
Abstract: Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, ...Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
#1: Journal: To be published
Title: The structure of the Cutibacterium acnes 70S ribosome
Authors: Lomakin, I.B. / Devarkar, S.C. / Grada, A. / Bunick, C.G.
History
DepositionMay 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
E: 30S ribosomal protein S5
G: 30S ribosomal protein S3
I: 30S ribosomal protein S7
J: 30S ribosomal protein S9
M: 30S ribosomal protein S10
N: 30S ribosomal protein S13
S: 30S ribosomal protein S14 type Z
U: 30S ribosomal protein S19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,40723
Polymers630,5639
Non-polymers84514
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
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 ribosomal RNA /


Mass: 498742.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: 2179609306

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30S ribosomal protein ... , 8 types, 8 molecules EGIJMNSU

#2: Protein 30S ribosomal protein S5 /


Mass: 22603.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5L8
#3: Protein 30S ribosomal protein S3 /


Mass: 29728.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5Y3
#4: Protein 30S ribosomal protein S7 /


Mass: 17615.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7ITZ4
#5: Protein 30S ribosomal protein S9 /


Mass: 18630.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JN42
#6: Protein 30S ribosomal protein S10 /


Mass: 11750.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A085B5E4
#7: Protein 30S ribosomal protein S13 /


Mass: 14030.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LKT6
#8: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6924.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMX1
#9: Protein 30S ribosomal protein S19 /


Mass: 10536.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7ITR7

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Non-polymers , 3 types, 14 molecules

#10: Chemical ChemComp-V7A / Sarecycline / Sarecycline


Mass: 487.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N3O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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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: 30S subunit head domain from 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Type: RIBOSOME / Entity ID: #1-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 30.56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4cryoSPARC3.3.1CTF correctionpatchCTF
7UCSF Chimera1.16model fitting
8Coot0.9.6 ELmodel fitting
10PHENIX1.20.1model refinement
11Coot0.9.6 ELmodel refinement
12cryoSPARC3.3.1initial Euler assignmentAb-initio
13cryoSPARC3.3.1final Euler assignment
15cryoSPARC3.3.13D reconstructionLocal Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1108852
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70853 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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