9PJ9 image
Deposition Date 2025-07-12
Release Date 2026-05-13
Last Version Date 2026-09-23
Entry Detail
PDB ID:
9PJ9
Keywords:
RIBOSOME
Title:
C. acnes 70S ribosome bound to Minocycline
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Thermus thermophilus (Taxon ID: 274)
Cutibacterium acnes (Taxon ID: 1747)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9PJ9 validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:A (auth: 0)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LJM0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:B (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7IDI8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:C (auth: 2)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:Q6A7V2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:D (auth: 3)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JN22
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:E (auth: 4)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JUW7
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:F (auth: A)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:G (auth: B)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I756
Polymer Type:polyribonucleotide
Molecule:initiator tRNA Met
Chain IDs:H (auth: C)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:I (auth: D)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JMY9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:J (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:Q6A6P3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:K (auth: F)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6L3A1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:L (auth: G)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I5Y3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:M (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7ITQ7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:N (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7ITZ4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:O (auth: J)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JN42
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:P (auth: K)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I645
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:Q (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LJN0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:R (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:Q6A6M5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:S (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LKT6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:T (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I743
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:U (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7IXM7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:V (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JMS7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:W (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LI71
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 typ
Gene (Uniprot):rpsN
Chain IDs:X (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JMX1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:Y (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I592
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:Z (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7ITR7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL37
Chain IDs:AA (auth: V)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A9Y2YAG1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:AURKAIP1/COX24 domain-contain
Gene (Uniprot):EII34_07160, EII35_08210, J5A53_13555
Chain IDs:BA (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A3N4D6F2
Polymer Type:polyribonucleotide
Molecule:mRNA 32MF
Chain IDs:CA (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:DA (auth: a)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:EA (auth: b)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:FA (auth: c)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JMV5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:GA (auth: d)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A1G9KW65
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:HA (auth: e)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I5M5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:IA (auth: f)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A3E2DDM1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:JA (auth: g)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I5S3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:KA (auth: i)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I6I7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:LA (auth: j)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JMZ8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:MA (auth: k)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7IUA0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:NA (auth: l)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I5M8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:OA (auth: m)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A8B2VJI7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:PA (auth: n)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JN02
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:QA (auth: o)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LKT3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:RA (auth: p)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I6V3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:SA (auth: q)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:Q6A9I3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:TA (auth: r)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7ITY5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:UA (auth: s)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2C6LEQ5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:VA (auth: t)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:Q6A6N7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:WA (auth: u)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7IYF8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:XA (auth: v)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7IGT1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:YA (auth: w)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I7B7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:ZA (auth: x)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7JB12
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:AB (auth: y)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I5Y4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:BB (auth: z)
Chain Length:0
Number of Molecules:1
Biological Source:Cutibacterium acnes
UniProt ID:A0A2B7I771
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MA DA A modified residue
2MG F G modified residue
3TD DA U modified residue
4OC F C modified residue
4SU H U modified residue
5MC F C modified residue
5MU H U modified residue
G7M F G modified residue
H2U DA U modified residue
MA6 F A modified residue
OMC DA C modified residue
OMG DA G modified residue
OMU DA U modified residue
PSU F U modified residue
UR3 F U modified residue
Ligand Molecules
MG
MIY
ZN
Primary Citation
Dual site targeting of the bacterial 70S ribosome by tetracyclines.
Nat Commun 17 ? ? (2026)
PMID: 42156748 DOI: 10.1038/s41467-026-72788-9

Abstact

The tetracycline class of antibiotics is widely used for treating bacterial diseases including Lyme disease, anthrax, acne vulgaris, and pneumonia. Using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we show that tetracyclines can simultaneously target the mRNA decoding center in the 30S subunit and the nascent peptide exit tunnel (NPET) in the 50S subunit of the bacterial ribosome. Among the tested tetracyclines, Doxycycline was distinct in its ability to dimerize and bind the NPET at multiple locations. Structural comparison of Doxycycline, Minocycline, and Sarecycline bound to the Escherichia coli and Cutibacterium acnes 70S ribosome revealed species-specific differences affecting drug interaction and occupancy. Our results reveal a dual site mechanism of action for tetracyclines and provide a structural basis for rational design of narrow spectrum tetracyclines to overcome the rising threat of antibiotic resistance.

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Protein

Chemical

Disease

Primary Citation of related structures
9PJ9
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