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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 / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / 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 L5, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S5, bacterial-type / 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 S14/S29 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 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 L33 / Ribosomal protein S18, conserved site / Ribosomal L28 family / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / 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: Devarkar, S.C. / Lomakin, I.B. / Bunick, C.G.
History
DepositionJul 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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