8E45

E. coli 50S ribosome bound to antibiotic analog SLC17

• PDB DOI: https://doi.org/10.2210/pdb8E45/pdb
• EM Map EMD-27880: EMDB EMDataResource
• NAKB: 8E45

• Classification: RIBOSOME
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-17 Released: 2023-06-28 
• Deposition Author(s): Pellegrino, J., Lee, D.J., Fraser, J.S., Seiple, I.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SLC collection of antibiotic analogs

Yeon, S.K., Pellegrino, J., Lee, D.J., Seiple, I.B., Fraser, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A1B1C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,110.22 kDa 
• Atom Count: 73,918 
• Modelled Residue Count: 4,194 
• Deposited Residue Count: 4,201 
• Unique protein chains: 8
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	C [auth K]	271	Escherichia coli	Mutation(s): 0  Gene Names: rplB, b3317, JW3279
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	D [auth L]	144	Escherichia coli	Mutation(s): 0  Gene Names: rplO
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413  Go to UniProtKB:  P02413

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	E [auth M]	201	Escherichia coli	Mutation(s): 0  Gene Names: rplD, ECMG_02584
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	F [auth N]	209	Escherichia coli	Mutation(s): 0  Gene Names: rplC, b3320, JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	G [auth O]	142	Escherichia coli	Mutation(s): 0  Gene Names: rplM, A1UI_03510
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	H [auth P]	110	Escherichia coli	Mutation(s): 0  Gene Names: rplV, eryB, b3315, JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	I [auth Q]	56	Escherichia coli	Mutation(s): 0  Gene Names: rpmF, ECDEC2D_1303
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	J [auth R]	46	Escherichia coli	Mutation(s): 0  Gene Names: rpmH
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	A [auth I]	2,904	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	B [auth J]	118	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UI6 (Subject of Investigation/LOI)	K [auth I]	2-{[(2S,3R,4S,6R)-2-{[(2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-13-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-3,5,6,8,10,12,14-heptamethyl-15-oxo-1-oxa-6-azacyclopentadecan-11-yl]oxy}-3-hydroxy-6-methyloxan-4-yl](methyl)amino}-N-{[(5S)-3-{(4M)-3-fluoro-4-[(6P)-6-(2-methyl-2H-tetrazol-5-yl)pyridin-3-yl]phenyl}-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide (non-preferred name) C56 H86 F N9 O15 CCCPNDPSMZJBSW-DALIEQGVSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Pellegrino, J., Lee, D.J., Fraser, J.S., Seiple, I.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM128656

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Data collection