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- PDB-8crx: Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarec... -

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Basic information

Entry
Database: PDB / ID: 8crx
TitleCutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 32MF mRNA
  • 5S ribosomal RNA
  • P-site initiator tRNA
  • RNA (1537-MER)
KeywordsANTIBIOTIC / ribosome / sarecycline / acne
Function / homology
Function and homology information


ribosomal large subunit assembly / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / tRNA binding ...ribosomal large subunit assembly / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 ...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 L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / 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 L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L21-like / L21-like superfamily
Similarity search - Domain/homology
Sarecycline / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 ...Sarecycline / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 30S ribosomal protein S10 / 50S ribosomal protein L3 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5 / 50S ribosomal protein L4 / 50S ribosomal protein L16 / 50S ribosomal protein L6 / Small ribosomal subunit protein uS3 / 50S ribosomal protein L30 / Small ribosomal subunit protein uS11 / 50S ribosomal protein L13 / 50S ribosomal protein L20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / 50S ribosomal protein L32 / 50S ribosomal protein L28 / 50S ribosomal protein L34 / 50S ribosomal protein L27 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / 50S ribosomal protein L22 / Small ribosomal subunit protein uS7 / 50S ribosomal protein L15 / Small ribosomal subunit protein bS16 / 50S ribosomal protein L25 / 50S ribosomal protein L29 / Small ribosomal subunit protein uS17 / 50S ribosomal protein L2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS4 / 50S ribosomal protein L14 / 50S ribosomal protein L18 / 50S ribosomal protein L36 / Small ribosomal subunit protein uS9 / 50S ribosomal protein L31 / Small ribosomal subunit protein bS6 / 50S ribosomal protein L23 / Small ribosomal subunit protein bS18 / 50S ribosomal protein L33 / Small ribosomal subunit protein uS12 / 50S ribosomal protein L19 / Small ribosomal subunit protein uS13 / 50S ribosomal protein L35 / 50S ribosomal protein L5 / AURKAIP1/COX24 domain-containing protein
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLomakin, I.B. / Devarkar, S.C. / Bunick, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Almirall, LLCresearch grant United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.
Authors: Ivan B Lomakin / Swapnil C Devarkar / Shivali Patel / Ayman Grada / Christopher G Bunick /
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, ...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.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (1537-MER)
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
H: 30S ribosomal protein S8
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
O: 30S ribosomal protein S15
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
T: 30S ribosomal protein S20
P: 30S ribosomal protein S16
X: 30S ribosomal protein bS22
G: 30S ribosomal protein S3
I: 30S ribosomal protein S7
J: 30S ribosomal protein S9
M: 30S ribosomal protein S10
N: 30S ribosomal protein S13
S: 30S ribosomal protein S14 type Z
U: 30S ribosomal protein S19
B: 30S ribosomal protein S2
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: 50S ribosomal protein L17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
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: 50S ribosomal protein L35
4: 50S ribosomal protein L31
a: 23S ribosomal RNA
b: 5S ribosomal RNA
V: 50S ribosomal protein bL37
Y: 32MF mRNA
C: P-site initiator tRNA
3: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,282,924447
Polymers2,272,24154
Non-polymers10,684393
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules AabYC

#1: RNA chain RNA (1537-MER)


Mass: 498742.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: 2179609306
#49: RNA chain 23S ribosomal RNA /


Mass: 1002554.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria)
#50: RNA chain 5S ribosomal RNA /


Mass: 38770.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: GenBank: 2179609306
#52: RNA chain 32MF mRNA


Mass: 7115.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#53: RNA chain P-site initiator tRNA


Mass: 24846.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 732678099

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30S ribosomal protein ... , 20 types, 20 molecules DEFHKLOQRTPXGIJMNSUB

#2: 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
#3: Protein 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: A0A2B7I5L8
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: Protein/peptide 30S ribosomal protein bS22 / / 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: A0A533INE0
#14: 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
#15: 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
#16: 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
#17: Protein 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: A0A085B5E4
#18: 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
#19: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6924.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A2B7JMX1
#20: 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
#21: 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

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50S ribosomal protein ... , 29 types, 29 molecules cdefgijklmnopqrstuvwxyz0124V3

#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: Protein 50S ribosomal protein L17 /


Mass: 20058.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cutibacterium acnes (bacteria) / References: UniProt: A0A085AZY3
#32: 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
#33: 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
#34: 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
#35: Protein 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: A0A085B4N9
#36: 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
#37: 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
#38: Protein 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: A0A085B5D2
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: Protein 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: A0A371N4N9
#48: 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
#51: 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)
#54: 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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Non-polymers , 4 types, 522 molecules

#55: Chemical ChemComp-V7A / Sarecycline / Sarecycline


Mass: 487.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N3O8 / Comment: medication, antibiotic*YM
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 386 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#58: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
Type: RIBOSOME / Entity ID: #1-#54 / 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
Specimen supportDetails: 25 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 30.56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.1particle selection
4cryoSPARC3.3.1CTF correctionpatchCTF
7UCSF Chimera1.16model fitting
8Coot0.9.6 ELmodel fitting
10PHENIX1.20.1model refinement
11Coot0.9.6 ELmodel refinement
12cryoSPARC3.3.1initial Euler assignmentAb-initio
13cryoSPARC3.3.1final Euler assignment
15cryoSPARC3.3.13D reconstructionNon-uniform Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1108852
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70853 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE

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