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- PDB-9i88: Structure of the wild-type Staphylococcus aureus 70S ribosome com... -

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Basic information

Entry
Database: PDB / ID: 9i88
TitleStructure of the wild-type Staphylococcus aureus 70S ribosome complexed with clincelin
Components
  • (Large ribosomal subunit protein ...) x 27
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 50S ribosomal protein L25
  • 5S ribosomal RNA
  • fMet-P-tRNA
KeywordsRIBOSOME / Antibiotic / Translation / Clincelin / Protein synthesis inhibitor / Staphylococcus aureus
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 / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L31 type B / 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 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...Ribosomal protein L31 type B / 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 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 L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / 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 L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / 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 L5, bacterial-type / 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 L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / 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 L28 family / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / 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 / : / Large ribosomal subunit protein uL24, C-terminal domain / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L17
Similarity search - Domain/homology
: / N-FORMYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL29 ...: / N-FORMYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsNovotna, M. / Boissier, F. / Balikova Novotna, G. / Innis, C.A.
Funding support Czech Republic, France, 4items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.2.69/0.0/0.0/18_053/0017705 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
Technology Agency of the Czech RepublicFW03010628 Czech Republic
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0012 RibioTiX France
CitationJournal: To Be Published
Title: Structure of the wild-type Staphylococcus aureus 70S ribosome complexed with clincelin
Authors: Novotna, M. / Slavik, P. / Demay, F. / Mahor, D. / Reha, D. / Boissier, F. / Pokorna, J. / Vimberg, V. / Brajerova, M. / Stefani, T. / Svoboda, J. / Gazak, R. / Marz, M. / Hosek, J. / ...Authors: Novotna, M. / Slavik, P. / Demay, F. / Mahor, D. / Reha, D. / Boissier, F. / Pokorna, J. / Vimberg, V. / Brajerova, M. / Stefani, T. / Svoboda, J. / Gazak, R. / Marz, M. / Hosek, J. / Koberska, M. / Eigner, V. / Hanzlikova, L. / Kuzma, M. / Krutova, M. / Kamenik, Z. / Sigut, K. / Janata, J. / Innis, C.A. / Balikova Novotna, G.
History
DepositionFeb 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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

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Assembly

Deposited unit
1: Large ribosomal subunit protein bL28
2: Large ribosomal subunit protein uL29
3: Large ribosomal subunit protein uL30
5: Large ribosomal subunit protein bL32
6: Large ribosomal subunit protein bL33A
7: Large ribosomal subunit protein bL34
8: Large ribosomal subunit protein bL35
9: Large ribosomal subunit protein bL36
B: 5S ribosomal RNA
D: fMet-P-tRNA
G: Large ribosomal subunit protein uL2
H: Large ribosomal subunit protein uL3
I: Large ribosomal subunit protein uL4
J: Large ribosomal subunit protein uL5
K: Large ribosomal subunit protein uL6
M: Large ribosomal subunit protein uL13
N: Large ribosomal subunit protein uL14
O: Large ribosomal subunit protein uL15
P: Large ribosomal subunit protein uL16
Q: Large ribosomal subunit protein bL17
R: Large ribosomal subunit protein uL18
S: Large ribosomal subunit protein bL19
T: Large ribosomal subunit protein bL20
U: Large ribosomal subunit protein bL21
V: Large ribosomal subunit protein uL22
W: Large ribosomal subunit protein uL23
X: Large ribosomal subunit protein uL24
Y: 50S ribosomal protein L25
Z: Large ribosomal subunit protein bL27
c: Small ribosomal subunit protein uS2
d: Small ribosomal subunit protein uS3
e: Small ribosomal subunit protein uS4
f: Small ribosomal subunit protein uS5
g: Small ribosomal subunit protein bS6
i: Small ribosomal subunit protein uS8
j: Small ribosomal subunit protein uS9
k: Small ribosomal subunit protein uS10
l: Small ribosomal subunit protein uS11
m: Small ribosomal subunit protein uS12
n: Small ribosomal subunit protein uS13
o: Small ribosomal subunit protein uS14B
p: Small ribosomal subunit protein uS15
q: Small ribosomal subunit protein bS16
r: Small ribosomal subunit protein uS17
s: Small ribosomal subunit protein bS18
t: Small ribosomal subunit protein uS19
u: Small ribosomal subunit protein bS20
4: Large ribosomal subunit protein bL31B
A: 23S ribosomal RNA
a: 16S ribosomal RNA
h: Small ribosomal subunit protein uS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,169,894443
Polymers2,159,45451
Non-polymers10,440392
Water00
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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Large ribosomal subunit protein ... , 27 types, 27 molecules 12356789GHIJKMNOPQRSTUVWXZ4

#1: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHL4
#2: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: A8Z349
#3: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ7
#4: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHV3
#5: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5944.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FYU6
#6: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FDE6
#7: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FG57
#8: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FER2
#11: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP2
#12: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEN9
#13: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP0
#14: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ1
#15: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ4
#16: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FES1
#17: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP9
#18: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ8
#19: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP6
#20: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FER6
#21: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ5
#22: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHJ7
#23: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FG58
#24: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FG80
#25: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP4
#26: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP1
#27: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ0
#29: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FG82
#48: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FF08

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RNA chain , 4 types, 4 molecules BDAa

#9: RNA chain 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: GenBank: CP020619.1
#10: RNA chain fMet-P-tRNA


Mass: 24788.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2
#49: RNA chain 23S ribosomal RNA


Mass: 946697.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: GenBank: CP020619.1
#50: RNA chain 16S ribosomal RNA


Mass: 502058.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: GenBank: CP020619.1

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Protein , 1 types, 1 molecules Y

#28: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FJE0

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Small ribosomal subunit protein ... , 19 types, 19 molecules cdefgijklmnopqrstuh

#30: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHI2
#31: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP5
#32: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FG18
#33: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ6
#34: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FJP8
#35: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ3
#36: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14642.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: A6QJ59
#37: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEN8
#38: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FER4
#39: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FJ95
#40: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FER3
#41: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEQ2
#42: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHG5
#43: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FHK0
#44: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP8
#45: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FJP6
#46: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FEP3
#47: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FGD8
#51: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: JE2 / References: UniProt: Q2FJ94

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Non-polymers , 5 types, 392 molecules

#52: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 383 / Source method: obtained synthetically / Formula: Mg
#54: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#55: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#56: Chemical ChemComp-A1I09 / Clincelin / 2-[(2R,3R,4S,5R,6R)-6-[(1S,2S)-2-chloranyl-1-[[(2S,4R)-1-methyl-4-propyl-pyrrolidin-2-yl]carbonylamino]propyl]-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanylethyl 2-oxidanylbenzoate


Mass: 575.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39ClN2O8S / Feature type: SUBJECT OF INVESTIGATION

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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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of the wild-type Staphylococcus aureus 70S ribosome complexed with clincelinRIBOSOME#1-#510NATURAL
250SCOMPLEX#1-#9, #11-#29, #48-#491NATURAL
330SCOMPLEX#30-#47, #50-#511NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Staphylococcus aureus (bacteria)1280JE2
22Staphylococcus aureus (bacteria)1280JE2
33Staphylococcus aureus (bacteria)1280JE2
Buffer solutionpH: 7.5
Details: 20 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 50 mM NH4Cl, 0.1 mM EDTA, pH 8, 6 mM beta-mercaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blotting time 2.5 s Blot force 5 Waiting time 30 s

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 400 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4008

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2SerialEMimage acquisition
4RELION4CTF correction
7UCSF Chimera1.7model fitting
8ISOLDE1.7model fitting
9Coot0.9.8.1model fitting
10PHENIX1.20.1-4487model fitting
12PHENIX1.20.1-4487model refinement
13RELION4initial Euler assignment
14RELION4final Euler assignment
15RELION4classification
16RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 389149
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61266 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7NHM

7nhm


Accession code: 7NHM / Source name: PDB / Type: experimental model

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