8E46 | pdb_00008e46

E. coli 50S ribosome bound to antibiotic analog SLC21

PDB DOI: https://doi.org/10.2210/pdb8E46/pdb
NAKB: 8E46
EM Map EMD-27881: EMDB EMDataResource

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

SLC collection of antibiotic analogs

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

To be published.

Macromolecule Content

Total Structure Weight: 1,110.15 kDa
Atom Count: 73,945
Modeled Residue Count: 4,194
Deposited Residue Count: 4,201
Unique protein chains: 8
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60422
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02413
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60723
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60438
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AA10
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61175
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7N4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7P5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

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

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(by identity cutoff)

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UHP (Subject of Investigation/LOI) Query on UHP Download:Ideal Coordinates CCD File SDF format, chain K [auth I] MOL2 format, chain K [auth I] mmCIF format, chain K [auth I]	K [auth I]	(2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-({3,4,6-trideoxy-3-[{[1-(2-{[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]amino}-2-oxoethyl)-1H-1,2,3-triazol-4-yl]methyl}(methyl)amino]-beta-D-xylo-hexopyranosyl}oxy)-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside C₅₁ H₈₅ N₇ O₁₇ CFLQVSVZEFCGKJ-DBMBZOQASA-N		Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-28

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2023-06-28
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection
Version 2.0: 2025-03-19
Changes: Atomic model, Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8E46 | pdb_00008e46

E. coli 50S ribosome bound to antibiotic analog SLC21

Literature

SLC collection of antibiotic analogs

Biological Assembly 1

Macromolecules

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 1

Sequence Annotations

Entity ID: 2

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)