8E3O

E. coli 50S ribosome bound to solithromycin and VM1

PDB DOI: https://doi.org/10.2210/pdb8E3O/pdb
EM Map EMD-27869: EMDB EMDataResource
NAKB: 8E3O

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: 1.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Solithromycin siderophore conjugates

Boyce, J.H., Pellegrino, J., Lee, D.J., Ecker, A.K., Seiple, I.B., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 1,110.45 kDa
Atom Count: 73,893
Modelled Residue Count: 4,194
Deposited Residue Count: 4,201
Unique protein chains: 8
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60422
Sequence Annotations Expand
Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02413
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Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60723
Sequence Annotations Expand
Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60438
Sequence Annotations Expand
Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AA10
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Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61175
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Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7N4
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Reference Sequence LOADING

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7P5
Sequence Annotations Expand
Reference Sequence LOADING

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EM1 (Subject of Investigation/LOI) Query on EM1 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]	(3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside C₄₃ H₆₅ F N₆ O₁₀ IXXFZUPTQVDPPK-ZAWHAJPISA-N		Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]
VIR (Subject of Investigation/LOI) Query on VIR Download Ideal Coordinates CCD File SDF format, chain L [auth I] MOL2 format, chain L [auth I] mmCIF format, chain L [auth I]	L [auth I]	VIRGINIAMYCIN M1 C₂₈ H₃₅ N₃ O₇ DAIKHDNSXMZDCU-FQTGFAPKSA-N		Interactions Focus chain L [auth I] Interactions & Density Focus chain L [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

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

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.

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Help and Resources

8E3O

E. coli 50S ribosome bound to solithromycin and VM1

Solithromycin siderophore conjugates

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

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)