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- PDB-9rfw: Manikomycin bound to the Escherichia coli 50S ribosomal subunit -

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Basic information

Entry
Database: PDB / ID: 9rfw
TitleManikomycin bound to the Escherichia coli 50S ribosomal subunit
Components
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 27
  • 23S rRNA
  • 5S rRNA
  • A-site tRNA-Phe
  • Manikomycin
  • P-site tRNA-Val
KeywordsANTIBIOTIC / Dal2 / PrAMP / Ribosome / Translation / Initiation / Nascent polypeptide exit tunnel / Cryo-EM
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity ...negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / 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 / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. ...Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / 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 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 L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / 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 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / 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 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Streptomyces rimosus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 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 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: Large ribosomal subunit protein bL36A
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
l: Large ribosomal subunit protein uL16
z: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL31A
a: 23S rRNA
b: 5S rRNA
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
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
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
Y: A-site tRNA-Phe
Z: P-site tRNA-Val
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
C: Manikomycin
D: Manikomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,407,544252
Polymers1,402,15835
Non-polymers5,386217
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 3cdlz4012fhijmnpqrvwxyegost

#1: 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
#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#23: 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
#24: 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
#25: 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
#26: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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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RNA chain , 4 types, 4 molecules abYZ

#7: 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)
#8: 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
#27: RNA chain A-site tRNA-Phe


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


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

#16: 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
#22: 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 CD

#34: 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 , 4 types, 282 molecules

#35: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Source: (natural) Streptomyces rimosus (bacteria)
#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 213 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#38: 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 50S ribosomal subunit / Type: RIBOSOME
Entity ID: #9-#11, #1, #6, #27-#28, #7-#8, #2-#3, #29, #12, #30, #13-#16, #4, #17-#18, #31, #19-#21, #32-#33, #22-#26, #5
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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251301 / Symmetry type: POINT
RefinementResolution: 2.4→2.4 Å / Cor.coef. Fo:Fc: 0.86 / WRfactor Rwork: 0.286 / SU B: 5.099 / SU ML: 0.107 / Average fsc free: 0 / Average fsc overall: 0.8776 / Average fsc work: 0.8776 / ESU R: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.2857 1816327 -
all0.286 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 62.599 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01197408
ELECTRON MICROSCOPYr_bond_other_d00.01854848
ELECTRON MICROSCOPYr_angle_refined_deg1.1191.846146035
ELECTRON MICROSCOPYr_angle_other_deg0.371.731129684
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.94753074
ELECTRON MICROSCOPYr_dihedral_angle_2_deg7.3255326
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg0.35352432
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.617104763
ELECTRON MICROSCOPYr_dihedral_angle_6_deg13.519101047
ELECTRON MICROSCOPYr_chiral_restr0.0490.218742
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.0265816
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0217353
ELECTRON MICROSCOPYr_nbd_refined0.1580.212163
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1950.251396
ELECTRON MICROSCOPYr_nbtor_refined0.2290.237797
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0790.233986
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.140.21906
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0560.28
ELECTRON MICROSCOPYr_mcbond_it5.5246.01912415
ELECTRON MICROSCOPYr_mcbond_other5.5246.01912415
ELECTRON MICROSCOPYr_mcangle_it8.11110.83515451
ELECTRON MICROSCOPYr_mcangle_other8.1110.83515452
ELECTRON MICROSCOPYr_scbond_it6.4286.32284993
ELECTRON MICROSCOPYr_scbond_other6.4276.32284994
ELECTRON MICROSCOPYr_scangle_it10.07211.468130581
ELECTRON MICROSCOPYr_scangle_other10.07211.468130582
ELECTRON MICROSCOPYr_lrange_it14.40669.716121747
ELECTRON MICROSCOPYr_lrange_other14.40669.721121732
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
2.45-2.5141.4161345111.4161345110.581.416
2.514-2.5830.9651310150.9651310150.6960.965
2.583-2.6570.7351275300.7351275300.7740.735
2.657-2.7390.5451236200.5451236200.8290.545
2.739-2.8290.4051197910.4051197910.8660.405
2.829-2.9280.3021161180.3021161180.8990.302
2.928-3.0390.231118290.231118290.9290.23
3.039-3.1630.2021075750.2021075750.9520.202
3.163-3.3030.2031034170.2031034170.9660.203
3.303-3.4650.208986460.208986460.9710.208
3.465-3.6520.214939910.214939910.9710.214
3.652-3.8740.214887870.214887870.9710.214
3.874-4.1410.209832970.209832970.9680.209
4.141-4.4730.203776430.203776430.9620.203
4.473-4.8990.202714170.202714170.9550.202
4.899-5.4770.197646130.197646130.950.197
5.477-6.3240.215568670.215568670.9390.215
6.324-7.7440.265481440.265481440.9240.265
7.744-10.9470.354371660.354371660.9260.354
10.947-248.2440.55203500.55203500.9260.55

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