6YS5

Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head

PDB DOI: https://doi.org/10.2210/pdb6YS5/pdb
NAKB: 6YS5
EM Map EMD-10892: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Mutation(s): No

Deposited: 2020-04-21 Released: 2020-09-16
Deposition Author(s): Nicholson, D., Edwards, T.A., O'Neill, A.J., Ranson, N.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.

Nicholson, D., Edwards, T.A., O'Neill, A.J., Ranson, N.A.

(2020) Structure 28: 1087-1100.e3

PubMed: 32857965 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.str.2020.08.004
Primary Citation of Related Structures:
6YHS, 6YPU, 6YS5, 6YSI, 6YT9, 6YTF

PubMed Abstract:
Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii.

Organizational Affiliation

Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.

Macromolecule Content

Total Structure Weight: 632.89 kDa
Atom Count: 16,864
Modelled Residue Count: 1,329
Deposited Residue Count: 2,572
Unique protein chains: 7
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	D [auth d]	250	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CD03 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CD03 Go to UniProtKB: D0CD03
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CD03
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	E [auth h]	156	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0C9P7 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0C9P7 Go to UniProtKB: D0C9P7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0C9P7
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	F [auth j]	128	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CG36 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CG36 Go to UniProtKB: D0CG36
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CG36
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	G [auth k]	103	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CCZ6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CCZ6 Go to UniProtKB: D0CCZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CCZ6
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	H [auth n]	118	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CD19 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CD19 Go to UniProtKB: D0CD19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CD19
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	I [auth o]	101	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CD10 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CD10 Go to UniProtKB: D0CD10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CD10
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	J [auth t]	91	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0
UniProt
Find proteins for D0CD01 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CD01 Go to UniProtKB: D0CD01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0CD01
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Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth 3]	1,544	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
E-site tRNA	B [auth 7]	77	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
mRNA	C [auth 9]	4	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth 3] SDF format, chain BA [auth 3] SDF format, chain CA [auth 3] SDF format, chain DA [auth 3] SDF format, chain EA [auth 3] SDF format, chain FA [auth 3] SDF format, chain GA [auth j] SDF format, chain HA [auth n] SDF format, chain K [auth 3] SDF format, chain L [auth 3] SDF format, chain M [auth 3] SDF format, chain N [auth 3] SDF format, chain O [auth 3] SDF format, chain P [auth 3] SDF format, chain Q [auth 3] SDF format, chain R [auth 3] SDF format, chain S [auth 3] SDF format, chain T [auth 3] SDF format, chain U [auth 3] SDF format, chain V [auth 3] SDF format, chain W [auth 3] SDF format, chain X [auth 3] SDF format, chain Y [auth 3] SDF format, chain Z [auth 3] MOL2 format, chain AA [auth 3] MOL2 format, chain BA [auth 3] MOL2 format, chain CA [auth 3] MOL2 format, chain DA [auth 3] MOL2 format, chain EA [auth 3] MOL2 format, chain FA [auth 3] MOL2 format, chain GA [auth j] MOL2 format, chain HA [auth n] MOL2 format, chain K [auth 3] MOL2 format, chain L [auth 3] MOL2 format, chain M [auth 3] MOL2 format, chain N [auth 3] MOL2 format, chain O [auth 3] MOL2 format, chain P [auth 3] MOL2 format, chain Q [auth 3] MOL2 format, chain R [auth 3] MOL2 format, chain S [auth 3] MOL2 format, chain T [auth 3] MOL2 format, chain U [auth 3] MOL2 format, chain V [auth 3] MOL2 format, chain W [auth 3] MOL2 format, chain X [auth 3] MOL2 format, chain Y [auth 3] MOL2 format, chain Z [auth 3]	AA [auth 3] BA [auth 3] CA [auth 3] DA [auth 3] EA [auth 3] AA [auth 3], BA [auth 3], CA [auth 3], DA [auth 3], EA [auth 3], FA [auth 3], GA [auth j], HA [auth n], K [auth 3], L [auth 3], M [auth 3], N [auth 3], O [auth 3], P [auth 3], Q [auth 3], R [auth 3], S [auth 3], T [auth 3], U [auth 3], V [auth 3], W [auth 3], X [auth 3], Y [auth 3], Z [auth 3]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth 3] Focus chain BA [auth 3] Focus chain CA [auth 3] Focus chain DA [auth 3] Focus chain EA [auth 3] Focus chain FA [auth 3] Focus chain GA [auth j] Focus chain HA [auth n] Focus chain K [auth 3] Focus chain L [auth 3] Focus chain M [auth 3] Focus chain N [auth 3] Focus chain O [auth 3] Focus chain P [auth 3] Focus chain Q [auth 3] Focus chain R [auth 3] Focus chain S [auth 3] Focus chain T [auth 3] Focus chain U [auth 3] Focus chain V [auth 3] Focus chain W [auth 3] Focus chain X [auth 3] Focus chain Y [auth 3] Focus chain Z [auth 3] Interactions & Density Focus chain AA [auth 3] Focus chain BA [auth 3] Focus chain CA [auth 3] Focus chain DA [auth 3] Focus chain EA [auth 3] Focus chain FA [auth 3] Focus chain GA [auth j] Focus chain HA [auth n] Focus chain K [auth 3] Focus chain L [auth 3] Focus chain M [auth 3] Focus chain N [auth 3] Focus chain O [auth 3] Focus chain P [auth 3] Focus chain Q [auth 3] Focus chain R [auth 3] Focus chain S [auth 3] Focus chain T [auth 3] Focus chain U [auth 3] Focus chain V [auth 3] Focus chain W [auth 3] Focus chain X [auth 3] Focus chain Y [auth 3] Focus chain Z [auth 3]