7P3W

F1Fo-ATP synthase from Acinetobacter baumannii (state 3)

PDB DOI: https://doi.org/10.2210/pdb7P3W/pdb
EM Map EMD-13186: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Acinetobacter baumannii ATCC 17978
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-07-08 Released: 2022-02-02
Deposition Author(s): Demmer, J.K., Phillips, B.P., Uhrig, O.L., Filloux, A., Allsopp, L.P., Bublitz, M., Meier, T.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii.

Demmer, J.K., Phillips, B.P., Uhrig, O.L., Filloux, A., Allsopp, L.P., Bublitz, M., Meier, T.

(2022) Sci Adv 8: eabl5966-eabl5966

PubMed: 35171679 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abl5966
Primary Citation of Related Structures:
7P2Y, 7P3N, 7P3W

PubMed Abstract:
The global spread of multidrug-resistant Acinetobacter baumannii infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the F ₁F _o-adenosine 5'-triphosphate (ATP) synthase from A. baumannii in three distinct conformational states. The nucleotide-converting F ₁ subcomplex reveals a specific self-inhibition mechanism, which supports a unidirectional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded F _o complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next-generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen.

Organizational Affiliation

Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK.

Macromolecule Content

Total Structure Weight: 535.71 kDa
Atom Count: 37,149
Modelled Residue Count: 4,900
Deposited Residue Count: 4,953
Unique protein chains: 8

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	514	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for A3M142 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M142 Go to UniProtKB: A3M142
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M142
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F	464	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for A3M144 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M144 Go to UniProtKB: A3M144
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M144
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit c	G H I [auth J] J [auth K] K [auth L] G, H, I [auth J], J [auth K], K [auth L], L [auth O], M [auth P], N [auth Q], O [auth R], P [auth S]	81	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M139 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M139 Go to UniProtKB: A3M139
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M139
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	Q [auth a]	291	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M137 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M137 Go to UniProtKB: A3M137
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M137
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	R [auth b], V [auth p]	156	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M140 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M140 Go to UniProtKB: A3M140
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M140
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	S [auth d]	178	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M141 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M141 Go to UniProtKB: A3M141
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M141
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	T [auth e]	139	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M145 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M145 Go to UniProtKB: A3M145
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M145
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	U [auth g]	289	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A3M143 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M143 Go to UniProtKB: A3M143
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M143
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain W [auth A] SDF format, chain Y [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth B]	AA [auth C], W [auth A], Y [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain W [auth A] Focus chain Y [auth B]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain CA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain CA [auth F]	CA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth F] Interactions & Density Focus chain CA [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth F] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth F] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth F] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth B]	BA [auth C], DA [auth F], X [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth F] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth F] Focus chain X [auth A] Focus chain Z [auth B]