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- PDB-8e3l: E. coli 50S ribosome bound to D-linker solithromycin conjugate -

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Basic information

Entry
Database: PDB / ID: 8e3l
TitleE. coli 50S ribosome bound to D-linker solithromycin conjugate
Components
  • (50S ribosomal protein ...) x 8
  • 50S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / E. coli ribosome / solithromycin / siderophore conjugate / antibiotics
Function / homology
Function and homology information


DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / 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 L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 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 L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 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 L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / 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 L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L3, conserved site / 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-UK3 / : / 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-UK3 / : / 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: 2.35 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: Solithromycin siderophore conjugates
Authors: Boyce, J.H. / Pellegrino, J. / Lee, D.J. / Ecker, A.K. / Seiple, I.B. / Fraser, J.S.
History
DepositionAug 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 28, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 2.0Mar 19, 2025Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _em_admin.last_update
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: 50S 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)1,111,10211
Polymers1,109,07810
Non-polymers2,0241
Water00
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 50S 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) / Strain: K12 / 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 , 1 types, 1 molecules

#11: Chemical ChemComp-UK3 / (2~{R})-~{N}-[(2~{R})-6-azanyl-1-[[(2~{R})-1-[[(2~{R})-1-[[3-[1-[4-[(1~{S},2~{R},5~{S},7~{R},8~{R},9~{R},11~{R},13~{R},14~{R})-8-[(2~{S},3~{R},4~{S},6~{R})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-2-ethyl-5-fluoranyl-9-methoxy-1,5,7,11,13-pentamethyl-4,6,12,16-tetrakis(oxidanylidene)-3,17-dioxa-15-azabicyclo[12.3.0]heptadecan-15-yl]butyl]-1,2,3-triazol-4-yl]phenyl]amino]-4-methylsulfanyl-1-oxidanylidene-butan-2-yl]amino]-3-(4-hydroxyphenyl)-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-hexan-2-yl]-1-[(2~{R})-2-[[(2~{R})-2-[2-[[2,3-bis(oxidanyl)phenyl]carbonyl-[4-[[2,3-bis(oxidanyl)phenyl]carbonylamino]butyl]amino]ethanoylamino]-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-oxidanyl-propanoyl]pyrrolidine-2-carboxamide


Mass: 2024.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C101H135FN16O25S / 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

ComponentName: 50S E. coli ribosome / Type: RIBOSOME / Entity ID: #2-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)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: 1000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 69 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: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105104 / Symmetry type: POINT

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