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- PDB-9c4g: Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound -

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Basic information

Entry
Database: PDB / ID: 9c4g
TitleCutibacterium acnes 50S ribosomal subunit with Clindamycin bound
Components
  • (50S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 4
  • 23S rRNA
  • 5S rRNA
KeywordsANTIBIOTIC / ribosome / clindamycin / acne
Function / homology
Function and homology information


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 ...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 / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / 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 L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 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. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L5 domain superfamily / Ribosomal protein L6, alpha-beta domain
Similarity search - Domain/homology
CLINDAMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 ...CLINDAMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL17 / 50S ribosomal protein bL37 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLomakin, I.B. / Devarkar, S.C. / Bunick, C.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Ortho Dermatologics Canada
CitationJournal: J Invest Dermatol / Year: 2024
Title: Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin.
Authors: Ivan B Lomakin / Swapnil C Devarkar / Ayman Grada / Christopher G Bunick /
Abstract: Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous-unit inflammation, are the main targets of antibiotic-based ...Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous-unit inflammation, are the main targets of antibiotic-based therapy against acne vulgaris (acne). The most widely used antibiotics in acne therapy are tetracyclines, macrolides, and lincosamides. Unfortunately, C. acnes bacteria over the past several decades have demonstrated increased resistance to these antibiotics, particularly to clindamycin. The precise knowledge of how antibiotics interact with their clinical target is needed to overcome this problem. Toward this goal, we determined the structure of clindamycin in complex with the ribosome of C. acnes at 2.53 Å resolution using cryogenic electron microscopy. The galactose sugar moiety of clindamycin interacts with nucleotides of the 23S ribosomal RNA directly or through a conserved network of water-mediated interactions. Its propyl pyrrolidinyl group interacts with the 23S ribosomal RNA through van der Waals forces. Clindamycin binding to the C. acnes ribosome interferes with both: proper orientation of the aminoacyl group of the A-site bound transfer RNA that is needed for peptide bond formation and with the extension of the nascent peptide. Our data are important for advancing the understanding of antibiotic resistance and development of narrow-spectrum antibacterial drugs, which is an urgent need for contemporary antibiotic stewardship.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
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Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
c: 50S ribosomal protein L2
d: 50S ribosomal protein L3
e: 50S ribosomal protein L4
f: 50S ribosomal protein L5
g: 50S ribosomal protein L6
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16
m: Large ribosomal subunit protein bL17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: Large ribosomal subunit protein bL21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: Large ribosomal subunit protein uL24
u: 50S ribosomal protein L25
v: 50S ribosomal protein L27
w: 50S ribosomal protein L28
x: 50S ribosomal protein L29
y: 50S ribosomal protein L30
z: 50S ribosomal protein L32
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: Large ribosomal subunit protein bL35
4: 50S ribosomal protein L31
a: 23S rRNA
b: 5S rRNA
V: 50S ribosomal protein bL37
3: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,448,522283
Polymers1,441,83231
Non-polymers6,690252
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 25 types, 25 molecules cdefgijklnoprsuvwxyz014V3

#1: Protein 50S ribosomal protein L2


Mass: 30309.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMV5
#2: Protein 50S ribosomal protein L3


Mass: 23553.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A1G9KW65
#3: Protein 50S ribosomal protein L4


Mass: 32342.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5M5
#4: Protein 50S ribosomal protein L5


Mass: 23901.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A3E2DDM1
#5: Protein 50S ribosomal protein L6


Mass: 19868.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5S3
#6: Protein 50S ribosomal protein L13


Mass: 16325.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I6I7
#7: Protein 50S ribosomal protein L14


Mass: 13503.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMZ8
#8: Protein 50S ribosomal protein L15


Mass: 15542.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7IUA0
#9: Protein 50S ribosomal protein L16


Mass: 15700.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5M8
#11: Protein 50S ribosomal protein L18


Mass: 13727.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JN02
#12: Protein 50S ribosomal protein L19


Mass: 13106.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LKT3
#13: Protein 50S ribosomal protein L20


Mass: 13988.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I6V3
#15: Protein 50S ribosomal protein L22


Mass: 16729.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7ITY5
#16: Protein 50S ribosomal protein L23


Mass: 11349.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LEQ5
#18: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22349.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7IYF8
#19: Protein 50S ribosomal protein L27


Mass: 9540.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7IGT1
#20: Protein 50S ribosomal protein L28


Mass: 6953.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I7B7
#21: Protein 50S ribosomal protein L29


Mass: 8899.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JB12
#22: Protein 50S ribosomal protein L30


Mass: 6932.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I5Y4
#23: Protein 50S ribosomal protein L32


Mass: 6991.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I771
#24: Protein 50S ribosomal protein L33


Mass: 6725.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LJM0
#25: Protein/peptide 50S ribosomal protein L34


Mass: 5185.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7IDI8
#27: Protein 50S ribosomal protein L31


Mass: 7731.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JUW7
#30: Protein/peptide 50S ribosomal protein bL37


Mass: 2744.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A9Y2YAG1
#31: Protein/peptide 50S ribosomal protein L36


Mass: 4386.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JN22

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Large ribosomal subunit protein ... , 4 types, 4 molecules mqt2

#10: Protein Large ribosomal subunit protein bL17


Mass: 20058.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A8B2VJI7
#14: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11087.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: Q6A9I3
#17: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 13514.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: loop 49-62 is not modeled, no EM density for it / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: Q6A6N7
#26: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7457.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: Q6A7V2

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RNA chain , 2 types, 2 molecules ab

#28: RNA chain 23S rRNA


Mass: 1002554.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: CP012350
#29: RNA chain 5S rRNA


Mass: 38770.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: 2179609306

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Non-polymers , 4 types, 408 molecules

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


Mass: 24.305 Da / Num. of mol.: 247 / Source method: obtained synthetically / Formula: Mg
#33: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#34: Chemical ChemComp-CLY / CLINDAMYCIN


Mass: 424.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33ClN2O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#35: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 50S subunit with Clindamycin bound / Type: RIBOSOME / Entity ID: #1-#31 / 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 38.58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2674133
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 283291 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00498834
ELECTRON MICROSCOPYf_angle_d0.608148524
ELECTRON MICROSCOPYf_dihedral_angle_d23.21448981
ELECTRON MICROSCOPYf_chiral_restr0.0418984
ELECTRON MICROSCOPYf_plane_restr0.0057597

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