9BYM | pdb_00009bym

Cryo-EM structure of ATP synthase non-stator state

PDB DOI: https://doi.org/10.2210/pdb9BYM/pdb
EM Map EMD-45038: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2024-05-23 Released: 2025-08-06
Deposition Author(s): Zhang, Z., Maharjan, R., Tringides, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.11 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

Cryo-EM structure of ATP synthase non-stator state

Zhang, Z., Maharjan, R., Tringides, M.

To be published.

Macromolecule Content

Total Structure Weight: 555.16 kDa
Atom Count: 29,873
Modeled Residue Count: 3,947
Deposited Residue Count: 5,173
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B [auth C], R [auth B]	550	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1XYK3 (Sus scrofa) Explore A0A8D1XYK3 Go to UniProtKB: A0A8D1XYK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1XYK3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	C [auth D], D [auth E], E [auth F]	570	Sus scrofa	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for A0A8D1JU29 (Sus scrofa) Explore A0A8D1JU29 Go to UniProtKB: A0A8D1JU29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1JU29
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase inhibitor, mitochondrial	F [auth J]	108	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q29307 (Sus scrofa) Explore Q29307 Go to UniProtKB: Q29307
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q29307
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G	273	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0YCC0 (Sus scrofa) Explore A0A8D0YCC0 Go to UniProtKB: A0A8D0YCC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D0YCC0
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit delta	H	168	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VPE5 (Sus scrofa) Explore A0A4X1VPE5 Go to UniProtKB: A0A4X1VPE5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VPE5
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit epsilon	I	136	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1L782 (Sus scrofa) Explore A0A8D1L782 Go to UniProtKB: A0A8D1L782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1L782
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase lipid-binding protein	J [auth K] K [auth L] L [auth N] M [auth O] N [auth P] J [auth K], K [auth L], L [auth N], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth M]	141	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1WGE8 (Sus scrofa) Explore A0A8D1WGE8 Go to UniProtKB: A0A8D1WGE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1WGE8
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 B] SDF format, chain S [auth A] SDF format, chain U [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain U [auth C]	AA [auth B], S [auth A], U [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth B] Focus chain S [auth A] Focus chain U [auth C] Interactions & Density Focus chain AA [auth B] Focus chain S [auth A] Focus chain U [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Y [auth F] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth F]	W [auth D], Y [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain W [auth D] Focus chain Y [auth F] Interactions & Density Focus chain W [auth D] Focus chain Y [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth F] MOL2 format, chain T [auth A] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain T [auth A] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth F]	T [auth A], V [auth C], X [auth D], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth F] Interactions & Density Focus chain T [auth A] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth F]