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- PDB-9rja: Manikomycin bound to the Escherichia coli 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 9rja
TitleManikomycin bound to the Escherichia coli 70S ribosome
Components
  • (30S ribosomal protein ...) x 5
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 27
  • (Small ribosomal subunit protein ...) x 15
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • A-site Phe-tRNA
  • Manikomycin
  • P-Site Val-tRNA
  • mRNA
KeywordsANTIBIOTIC / Manikomycin / Ribosome / E-site / Translation / Elongation / Cryo-EM
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / four-way junction DNA binding / negative regulation of cytoplasmic translation / DnaA-L2 complex / regulation of mRNA stability / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / regulation of DNA-templated transcription elongation / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / transcription antitermination / DNA endonuclease activity / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosome binding / 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 / response to antibiotic / negative regulation of DNA-templated transcription / hydrolase activity / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / 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 L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / 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 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
Similarity search - Domain/homology
: / : / PAROMOMYCIN / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 ...: / : / PAROMOMYCIN / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Streptomyces rimosus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsKaur, M. / Travin, D. / Berger, M.J. / Jangra, M. / Morici, M. / Safdari, H.A. / Guitor, A.K. / Koteva, K. / Xu, M. / Chen, X. ...Kaur, M. / Travin, D. / Berger, M.J. / Jangra, M. / Morici, M. / Safdari, H.A. / Guitor, A.K. / Koteva, K. / Xu, M. / Chen, X. / Vazquez-Laslop, N. / Mankin, A.S. / Wilson, D.N. / Wright, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 Germany
CitationJournal: Res Sq / Year: 2025
Title: A Natural Depsipeptide Antibiotic that Targets the E site of the Bacterial Ribosome.
Authors: Gerard Wright / Manpreet Kaur / Dmitrii Travin / Max Berger / Manoj Jangra / Martino Morici / Haaris Ahsan Safdari / Dorota Klepacki / Wenliang Wang / Michael Cook / Sommer Chou / Allison ...Authors: Gerard Wright / Manpreet Kaur / Dmitrii Travin / Max Berger / Manoj Jangra / Martino Morici / Haaris Ahsan Safdari / Dorota Klepacki / Wenliang Wang / Michael Cook / Sommer Chou / Allison Guitor / Kalinka Koteva / Min Xu / Linda Ejim / Lesley Macneil / Nora Vázquez-Laslop / Alexander Mankin / Daniel Wilson /
Abstract: A significant challenge in addressing the antibiotic resistance crisis is identifying new antimicrobial compounds. Although natural products produced by fungi and bacteria, particularly ...A significant challenge in addressing the antibiotic resistance crisis is identifying new antimicrobial compounds. Although natural products produced by fungi and bacteria, particularly actinomycetes, have been the source of most antibiotics discovered over the past 80 years, they have fallen out of favor due to the frequent rediscovery of known drug scaffolds. The current perception is that antibiotic-producing actinomycetes have been over-mined and possess little novelty left to yield. Here, we demonstrate that by using improved fractionation approaches that enrich previously overlooked minor products, even well-studied strains of antibiotic-producing actinomycetes can provide new chemical scaffolds with unique modes of action. By fractionating a library of natural product extracts from soil bacteria, we show that Streptomyces rimosus, the source of the well-known antibiotic oxytetracycline, produces a previously overlooked cyclic depsipeptide antibiotic that we called manikomycin. Manikomycin can kill multi-drug-resistant Enterobacteriaceae and is not susceptible to resistance associated with clinically used antibiotics. Biochemical, genetic, and structural analyses reveal that manikomycin binds in the 'exit' or E site of the large subunit of the bacterial ribosome preventing the entry of the 3' end of the tRNA into the E site and effectively hindering the translocation step of protein synthesis in a sequence context-specific manner. Manikomycin is the first antibacterial agent to target the critical but underexplored E site in the large ribosomal subunit, highlighting its value as a lead for developing new antibiotics.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
3: Large ribosomal subunit protein bL36A
C: Small ribosomal subunit protein uS3
E: Small ribosomal subunit protein uS5
F: 30S ribosomal protein S6, fully modified isoform
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: 30S ribosomal protein S16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
X: mRNA
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
f: Large ribosomal subunit protein uL5
h: Large ribosomal subunit protein bL9
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL14
k: 50S ribosomal protein L15
l: Large ribosomal subunit protein uL16
m: Large ribosomal subunit protein bL17
n: Large ribosomal subunit protein uL18
p: Large ribosomal subunit protein bL20
q: Large ribosomal subunit protein bL21
r: Large ribosomal subunit protein uL22
u: 50S ribosomal protein L25
v: Large ribosomal subunit protein bL27
w: Large ribosomal subunit protein bL28
x: Large ribosomal subunit protein uL29
y: Large ribosomal subunit protein uL30
z: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL31A
a: 23S rRNA
b: 5S rRNA
A: 16S rRNA
B: 30S ribosomal protein S2
D: Small ribosomal subunit protein uS4
G: 30S ribosomal protein S7
H: Small ribosomal subunit protein uS8
S: Small ribosomal subunit protein uS19
T: 30S ribosomal protein S20
U: Small ribosomal subunit protein bS21
e: Large ribosomal subunit protein uL4
g: Large ribosomal subunit protein uL6
o: Large ribosomal subunit protein bL19
s: Large ribosomal subunit protein uL23
t: Large ribosomal subunit protein uL24
Y: A-site Phe-tRNA
Z: P-Site Val-tRNA
V: Manikomycin
W: Manikomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,204,296373
Polymers2,195,67157
Non-polymers8,625316
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Large ribosomal subunit protein ... , 27 types, 27 molecules 0123cdfhijlmnpqrvwxyz4egost

#1: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7N9
#2: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7P5
#3: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7Q1
#4: Protein/peptide Large ribosomal subunit protein bL36A / 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7Q6
#19: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60422
#20: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60438
#21: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P62399
#22: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R1
#23: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AA10
#24: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADY3
#26: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15343.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADY7
#27: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG44
#28: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0C018
#29: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7L3
#30: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG48
#31: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P61175
#33: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7L8
#34: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M2
#35: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M6
#36: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG51
#37: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7N4
#38: Protein Large ribosomal subunit protein bL31A / 50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M9
#49: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60723
#50: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG55
#51: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7K6
#52: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADZ0
#53: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60624

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Small ribosomal subunit protein ... , 15 types, 15 molecules CEIJKLMNOQRDHSU

#5: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V3
#6: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W1
#8: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7X3
#9: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R5
#10: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13871.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R9
#11: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S3
#12: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S9
#13: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG59
#14: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADZ4
#16: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG63
#17: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T7
#43: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V8
#45: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W7
#46: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U3
#48: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68679

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30S ribosomal protein ... , 5 types, 5 molecules FPBGT

#7: Protein 30S ribosomal protein S6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#15: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3
#42: Protein 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#44: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359
#47: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7

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RNA chain , 6 types, 6 molecules XabAYZ

#18: RNA chain mRNA


Mass: 3774.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#39: RNA chain 23S rRNA


Mass: 941811.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#40: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1845258627
#41: RNA chain 16S rRNA


Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#54: RNA chain A-site Phe-tRNA


Mass: 24469.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#55: RNA chain P-Site Val-tRNA


Mass: 24483.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)

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50S ribosomal protein ... , 2 types, 2 molecules ku

#25: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02413
#32: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68919

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Protein/peptide , 1 types, 2 molecules VW

#56: Protein/peptide Manikomycin


Type: Cyclic depsipeptide / Class: Antimicrobial / Mass: 1205.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cyclic depsipeptide / Source: (natural) Streptomyces rimosus (bacteria) / References: BIRD: PRD_002603

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Non-polymers , 6 types, 381 molecules

#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#58: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 309 / Source method: obtained synthetically / Formula: Mg
#59: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#60: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: medication*YM
#61: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#62: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsManikomycin inhibits prokaryotic translation by targeting the E site of the large ribosomal subunit ...Manikomycin inhibits prokaryotic translation by targeting the E site of the large ribosomal subunit It can kill multi-drug-resistant Enterobacteriaceae and is not susceptible to resistance associated with clinically used antibiotics. Manikomycin binds the E site of the bacterial ribosome, blocking tRNA exit and halting translation in a sequence-specific manner.
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Manikomycin bound 70S E. coli ribosome / Type: RIBOSOME
Entity ID: #1-#4, #38, #41-#42, #5, #43, #6-#7, #44-#45, #8-#17, #46-#48, #18, #54-#55, #39-#40, #19-#20, #49, #21, #50, #22-#28, #51, #29-#31, #52-#53, #32-#37
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 mol/LPotassium acetateCH3COOK1
210 mmol/LMagnesium acetate(CH3COO)2Mg1
380 mmol/LAmmonium chlorideNH4Cl1
450 mmol/LHepesC8H18N2O4S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 defocus max: 1000 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5.0.0particle selection
2REFMAC5.8.0425model refinement
13RELION5.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 483608
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340201 / Symmetry type: POINT
RefinementResolution: 2.45→2.45 Å / Cor.coef. Fo:Fc: 0.874 / WRfactor Rwork: 0.284 / SU B: 5.975 / SU ML: 0.123 / Average fsc free: 0 / Average fsc overall: 0.8791 / Average fsc work: 0.8791 / ESU R: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.2837 2611103 -
all0.284 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 78.233 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.011152318
ELECTRON MICROSCOPYr_bond_other_d00.01788461
ELECTRON MICROSCOPYr_angle_refined_deg1.111.846227459
ELECTRON MICROSCOPYr_angle_other_deg0.3681.734208707
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.03855386
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.8035572
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg0.4753626
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.969108297
ELECTRON MICROSCOPYr_dihedral_angle_6_deg12.91910.0051876
ELECTRON MICROSCOPYr_chiral_restr0.0490.229072
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.02106268
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0227547
ELECTRON MICROSCOPYr_nbd_refined0.1710.221566
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2030.284789
ELECTRON MICROSCOPYr_nbtor_refined0.2290.260009
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.080.254713
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1490.23287
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.1020.255
ELECTRON MICROSCOPYr_metal_ion_refined0.0980.21
ELECTRON MICROSCOPYr_mcbond_it6.8417.4721759
ELECTRON MICROSCOPYr_mcbond_other6.8417.4721759
ELECTRON MICROSCOPYr_mcangle_it10.00813.43927079
ELECTRON MICROSCOPYr_mcangle_other10.00813.43927080
ELECTRON MICROSCOPYr_scbond_it8.3197.912130559
ELECTRON MICROSCOPYr_scbond_other8.3197.912130559
ELECTRON MICROSCOPYr_scangle_it12.9114.322200380
ELECTRON MICROSCOPYr_scangle_other12.9114.322200381
ELECTRON MICROSCOPYr_lrange_it19.4187.538191933
ELECTRON MICROSCOPYr_lrange_other19.40987.538191934
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.5-2.5651.3361934601.3361934600.5981.336
2.565-2.6350.931881720.931881720.7050.93
2.635-2.7120.7141832480.7141832480.7760.714
2.712-2.7950.5361779250.5361779250.8270.536
2.795-2.8870.41724250.41724250.8690.4
2.887-2.9880.2911665870.2911665870.9050.291
2.988-3.1010.2221610180.2221610180.9350.222
3.101-3.2270.21546080.21546080.9540.2
3.227-3.3710.2051485030.2051485030.9650.205
3.371-3.5350.2111420920.2111420920.9670.211
3.535-3.7270.2191348920.2191348920.9680.219
3.727-3.9530.2181274850.2181274850.9680.218
3.953-4.2250.2161200290.2161200290.9640.216
4.225-4.5640.2121115690.2121115690.9580.212
4.564-4.9990.2091025980.2091025980.9510.209
4.999-5.5890.204928070.204928070.9460.204
5.589-6.4540.22819560.22819560.9350.22
6.454-7.9030.265690790.265690790.9210.265
7.903-11.1730.336534360.336534360.9220.336
11.173-290.9880.492292240.492292240.9210.492

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