8CVO

Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.

Lomakin, I.B., Devarkar, S.C., Patel, S., Grada, A., Bunick, C.G.

(2023) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkad103
  • Primary Citation of Related Structures:  
    8CRX, 8CVM, 8CVO, 8CWO

  • PubMed 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, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy ...

    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.

    Related Citations: 
    • The structure of the Cutibacterium acnes 70S ribosome
      Lomakin, I.B., Devarkar, S.C., Grada, A., Bunick, C.G.
      () To be published --: --
    Organizational Affiliation: 

    Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5B [auth E]215Cutibacterium acnesMutation(s): 0 
Gene Names: rpsE, COH10_09895
UniProt
Find proteins for A0A2B7I5L8 (Cutibacterium acnes)
Explore A0A2B7I5L8 
Go to UniProtKB:  A0A2B7I5L8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2B7I5L8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth G]269Cutibacterium acnesMutation(s): 0 
Gene Names: rpsC, COH10_09950
UniProt
Find proteins for A0A2B7I5Y3 (Cutibacterium acnes)
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UniProt GroupA0A2B7I5Y3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7D [auth I]156Cutibacterium acnesMutation(s): 0 
Gene Names: rpsG, COH10_10055
UniProt
Find proteins for A0A2B7ITZ4 (Cutibacterium acnes)
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UniProt GroupA0A2B7ITZ4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9E [auth J]173Cutibacterium acnesMutation(s): 0 
Gene Names: rpsI, COH10_09690
UniProt
Find proteins for A0A2B7JN42 (Cutibacterium acnes)
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UniProt GroupA0A2B7JN42
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10F [auth M]103Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A085B5E4 (Cutibacterium acnes HL201PA1)
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UniProt GroupA0A085B5E4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13G [auth N]123Cutibacterium acnesMutation(s): 0 
Gene Names: rpsM, COH10_09820
UniProt
Find proteins for A0A2C6LKT6 (Cutibacterium acnes)
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UniProt GroupA0A2C6LKT6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZH [auth S]61Cutibacterium acnesMutation(s): 0 
Gene Names: rpsZ, rpsN, COH10_09915
UniProt
Find proteins for A0A2B7JMX1 (Cutibacterium acnes)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19I [auth U]93Cutibacterium acnesMutation(s): 0 
Gene Names: rpsS, COH10_09960, DI580_10860
UniProt
Find proteins for A0A2B7ITR7 (Cutibacterium acnes)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1,537Cutibacterium acnes
Protein Feature View
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V7A (Subject of Investigation/LOI)
Query on V7A
Download Ideal Coordinates CCD File 
J [auth A]Sarecycline
C24 H29 N3 O8
PQJQFLNBMSCUSH-SBAJWEJLSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
W [auth S]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.9.6 EL
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Almirall, LLCUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release