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- PDB-8e33: E. coli 50S ribosome bound to compound streptogramin analog SAB001 -

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Basic information

Entry
Database: PDB / ID: 8.0E+33
TitleE. coli 50S ribosome bound to compound streptogramin analog SAB001
Components
  • (50S ribosomal protein ...) x 8
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME/ANTIBIOTIC / E. coli ribosome / streptogramin A / streptogramin B / antibiotics / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation ...DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L32p, bacterial type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / : / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 ...Ribosomal protein L32p, bacterial type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / : / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L2 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L13 signature. / Ribosomal protein L2, domain 3 / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L22/L17 / Ribosomal protein L3, conserved site / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Zinc-binding ribosomal protein / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-UDU / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L4 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 ...Chem-UDU / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L4 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsPellegrino, J. / Lee, D.J. / Fraser, J.S. / Seiple, I.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128656 United States
CitationJournal: To Be Published
Title: Potential for clicked streptogramin analogs
Authors: Takahashi, Y. / Pellegrino, J. / Lee, D.J. / Fraser, J.S. / Seiple, I.B.
History
DepositionAug 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: 23S ribosomal RNA
J: 5S ribosomal RNA
K: 50S ribosomal protein L2
L: 50S ribosomal protein L15
M: 50S ribosomal protein L4
N: 50S ribosomal protein L3
O: 50S ribosomal protein L13
P: 50S ribosomal protein L22
Q: 50S ribosomal protein L32
R: 50S ribosomal protein L34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,110,50011
Polymers1,109,07810
Non-polymers1,4231
Water181
1


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

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Components

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RNA chain , 2 types, 2 molecules IJ

#1: RNA chain 23S ribosomal RNA


Mass: 941795.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: RNA chain 5S ribosomal RNA


Mass: 38177.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1266940032

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50S ribosomal protein ... , 8 types, 8 molecules KLMNOPQR

#3: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#4: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#5: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplD, ECMG_02584 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9FY55
#6: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#7: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, A1UI_03510 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EW51
#8: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#9: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, ECDEC2D_1303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828UBL8
#10: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4

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Non-polymers , 2 types, 2 molecules

#11: Chemical ChemComp-UDU / N-{(4R,6R,9S,10R,13S,15aS,17R,20R,22S,24aS)-22-benzyl-6-[2-(4-{[(3R,4R,5E,10E,12E,14S,16R,23S,26aR)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,3H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-4-yl]methyl}-1H-1,2,3-triazol-1-yl)ethyl]-17-hydroxy-10,23-dimethyl-5,8,12,15,21,24-hexaoxo-13-phenyldocosahydro-12H-pyrido[2,1-f]pyrrolo[2,1-l][1,4,7,10,13,16]oxapentaazacyclononadecin-9-yl}-3-hydroxypyridine-2-carboxamide


Mass: 1422.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C73H88FN13O16 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 50S E. coli ribosome / Type: RIBOSOME / Entity ID: #1-#10 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162125 / Symmetry type: POINT

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