9JC1 | pdb_00009jc1

Engineering of ATP synthase

PDB DOI: https://doi.org/10.2210/pdb9JC1/pdb
EM Map EMD-61339: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Bacillus sp. PS3
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-28 Released: 2025-07-09
Deposition Author(s): Hamaguchi-Suzuki, N., Ueno, H., Yasuda, K., Marui, R., Adachi, N., Senda, T., Noji, H., Murata, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Human Frontier Science Program (HFSP), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Engineering of ATP synthase for enhancement of proton-to-ATP ratio

Ueno, H., Yasuda, K., Hamaguchi-Suzuki, N., Marui, R., Adachi, N., Senda, T., Murata, T., Noji, H.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-025-61227-w

Macromolecule Content

Total Structure Weight: 505.74 kDa
Atom Count: 28,164
Modeled Residue Count: 3,905
Deposited Residue Count: 4,578
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	A [auth D], B [auth E], C [auth F]	484	Bacillus sp. PS3	Mutation(s): 0 Gene Names: uncD, atpD EC: 7.1.2.2
UniProt
Find proteins for A0A0M4U1P9 (Bacillus sp. (strain PS3)) Explore A0A0M4U1P9 Go to UniProtKB: A0A0M4U1P9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M4U1P9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	D [auth G]	285	Bacillus sp. PS3	Mutation(s): 0 Gene Names: uncG, atpG
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3)) Explore A0A0M4TPJ7 Go to UniProtKB: A0A0M4TPJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M4TPJ7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	E [auth H]	87	Bacillus sp. PS3	Mutation(s): 0 Gene Names: uncC, atpC
UniProt
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3)) Explore A0A0M5MQR7 Go to UniProtKB: A0A0M5MQR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M5MQR7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha	F [auth I], G [auth J], H [auth K]	580	Bacillus sp. PS3	Mutation(s): 3 EC: 7.1.2.2
UniProt
Find proteins for A0A0M3VGF9 (Bacillus sp. (strain PS3)) Explore A0A0M3VGF9 Go to UniProtKB: A0A0M3VGF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M3VGF9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	I [auth A], K [auth C], M	169	Bacillus sp. PS3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	J [auth B], L, N	169	Bacillus sp. PS3	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E] mmCIF format, chain O [auth E]	O [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain Q [auth I] SDF format, chain R [auth J] SDF format, chain S [auth K] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth I] MOL2 format, chain R [auth J] MOL2 format, chain S [auth K] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth I] mmCIF format, chain R [auth J] mmCIF format, chain S [auth K]	P [auth E], Q [auth I], R [auth J], S [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth K] Interactions & Density Focus chain P [auth E] Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth K]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H00388
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05624
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K18092
Human Frontier Science Program (HFSP)	France	RGP0054/2020
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121013
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101071