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- PDB-9pj9: C. acnes 70S ribosome bound to Minocycline -

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Basic information

Entry
Database: PDB / ID: 9pj9
TitleC. acnes 70S ribosome bound to Minocycline
Components
  • (30S ribosomal protein ...) x 17
  • (50S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 4
  • (Small ribosomal subunit protein ...) x 2
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • AURKAIP1/COX24 domain-containing protein
  • initiator tRNA Met
  • mRNA 32MF
KeywordsRIBOSOME / Tetracycline / bacterial ribosome / protein translation / Minocycline / Antibiotic / cutibacterium acnes
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / 50S ribosomal protein L37 helical region / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : ...: / 50S ribosomal protein L37 helical region / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S14/S29 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / :
Similarity search - Domain/homology
Chem-MIY / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 ...Chem-MIY / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / AURKAIP1/COX24 domain-containing protein / Large ribosomal subunit protein bL17 / 50S ribosomal protein bL37 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Cutibacterium acnes (bacteria)
Thermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDevarkar, S.C. / Lomakin, I.B. / Bunick, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2026
Title: Dual site targeting of the bacterial 70S ribosome by tetracyclines.
Authors: Swapnil C Devarkar / Ivan B Lomakin / Jimin Wang / Ayman Grada / Christopher G Bunick /
Abstract: 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 ...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.
History
DepositionJul 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: Large ribosomal subunit protein bL35
3: 50S ribosomal protein L36
4: 50S ribosomal protein L31
A: 16S rRNA
B: 30S ribosomal protein S2
C: initiator tRNA Met
D: 30S ribosomal protein S4
E: Small ribosomal subunit protein uS5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S3
H: 30S ribosomal protein S8
I: 30S ribosomal protein S7
J: 30S ribosomal protein S9
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: Small ribosomal subunit protein uS10
N: 30S ribosomal protein S13
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S14 type Z
T: 30S ribosomal protein S20
U: 30S ribosomal protein S19
V: 50S ribosomal protein bL37
X: AURKAIP1/COX24 domain-containing protein
Y: mRNA 32MF
a: 23S rRNA
b: 5S rRNA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,281,575387
Polymers2,271,93554
Non-polymers9,640333
Water1,65792
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 0134Vcdefgijklnoprsuvwxyz

#1: 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
#2: 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
#4: 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
#5: 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
#27: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#42: 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
#43: 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
#44: 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
#46: 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
#47: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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

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Large ribosomal subunit protein ... , 4 types, 4 molecules 2mqt

#3: 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
#41: 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
#45: 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
#48: 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 / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: Q6A6N7

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RNA chain , 5 types, 5 molecules ACYab

#6: RNA chain 16S rRNA


Mass: 498742.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: 2179609306
#8: RNA chain initiator tRNA Met


Mass: 24541.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1802457359
#29: RNA chain mRNA 32MF


Mass: 7115.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#30: 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
#31: 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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30S ribosomal protein ... , 17 types, 17 molecules BDFGHIJKLNOPQRSTU

#7: Protein 30S ribosomal protein S2


Mass: 31583.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I756
#9: Protein 30S ribosomal protein S4


Mass: 23271.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMY9
#11: Protein 30S ribosomal protein S6


Mass: 11270.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6L3A1
#12: 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
#13: Protein 30S ribosomal protein S8


Mass: 14677.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7ITQ7
#14: 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
#15: 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
#16: Protein 30S ribosomal protein S11


Mass: 14194.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I645
#17: Protein 30S ribosomal protein S12


Mass: 13666.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LJN0
#19: 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
#20: Protein 30S ribosomal protein S15


Mass: 10102.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I743
#21: Protein 30S ribosomal protein S16


Mass: 15980.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7IXM7
#22: Protein 30S ribosomal protein S17


Mass: 10475.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMS7
#23: Protein 30S ribosomal protein S18


Mass: 8817.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2C6LI71
#24: Protein 30S ribosomal protein S14 type Z


Mass: 6924.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMX1
#25: Protein 30S ribosomal protein S20


Mass: 9724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7I592
#26: 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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Small ribosomal subunit protein ... , 2 types, 2 molecules EM

#10: Protein Small ribosomal subunit protein uS5 / 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: Q6A6P3
#18: Protein Small ribosomal subunit protein uS10 / 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: Q6A6M5

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Protein/peptide , 1 types, 1 molecules X

#28: Protein/peptide AURKAIP1/COX24 domain-containing protein


Mass: 4120.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A3N4D6F2

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Non-polymers , 4 types, 425 molecules

#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 324 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: C. acnes 70S ribosome bound to Minocycline / Type: COMPLEX / Entity ID: #1-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cutibacterium acnes (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1UCSF ChimeraX1.10/v10model fitting
2cryoSPARCv4particle selection
3cryoSPARCv4CTF correction
4cryoSPARCv4initial Euler assignment
5cryoSPARCv4final Euler assignment
6cryoSPARCv43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105824 / Symmetry type: POINT

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