9BYK | pdb_00009byk

Cryo-EM structure of ATP synthase E state

PDB DOI: https://doi.org/10.2210/pdb9BYK/pdb
EM Map EMD-45036: 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: 3.03 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 E state

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

To be published.

Macromolecule Content

Total Structure Weight: 705.58 kDa
Atom Count: 37,263
Modeled Residue Count: 5,028
Deposited Residue Count: 6,505
Unique protein chains: 18

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase protein 8	A [auth 8]	67	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q35914 (Sus scrofa) Explore Q35914 Go to UniProtKB: Q35914
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q35914
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	AA [auth C], B [auth A], CA [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: 3
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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	F [auth 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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit delta	G [auth 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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit epsilon	H [auth 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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase inhibitor, mitochondrial	I [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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase lipid-binding protein	J [auth K] K [auth L] L [auth M] M [auth N] N [auth O] J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R]	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

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit O, mitochondrial	R [auth S]	213	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A2C9F3A3 (Sus scrofa) Explore A0A2C9F3A3 Go to UniProtKB: A0A2C9F3A3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2C9F3A3
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit	S [auth T]	103	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SAK7 (Sus scrofa) Explore F1SAK7 Go to UniProtKB: F1SAK7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1SAK7
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	T [auth a]	226	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q35915 (Sus scrofa) Explore Q35915 Go to UniProtKB: Q35915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q35915
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	U [auth b]	238	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1YQG6 (Sus scrofa) Explore A0A8D1YQG6 Go to UniProtKB: A0A8D1YQG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1YQG6
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase-coupling factor 6, mitochondrial	V [auth c]	76	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P13618 (Sus scrofa) Explore P13618 Go to UniProtKB: P13618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13618
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Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit d, mitochondrial	W [auth d]	166	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1FFA1 (Sus scrofa) Explore A0A8D1FFA1 Go to UniProtKB: A0A8D1FFA1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1FFA1
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit e, mitochondrial	X [auth e]	71	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q9MYT8 (Sus scrofa) Explore Q9MYT8 Go to UniProtKB: Q9MYT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9MYT8
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Reference Sequence

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| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase membrane subunit K, mitochondrial	Y [auth i]	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TQQ5 (Sus scrofa) Explore A0A4X1TQQ5 Go to UniProtKB: A0A4X1TQQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1TQQ5
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Reference Sequence

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| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
unkown protein	Z [auth k]	26	Sus scrofa	Mutation(s): 0

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| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit f, mitochondrial	BA [auth f]	88	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q95339 (Sus scrofa) Explore Q95339 Go to UniProtKB: Q95339
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q95339
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 LA [auth B] SDF format, chain JA [auth C] SDF format, chain DA [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain DA [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain DA [auth A]	DA [auth A], JA [auth C], LA [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain DA [auth A] Focus chain JA [auth C] Focus chain LA [auth B] Interactions & Density Focus chain DA [auth A] Focus chain JA [auth C] Focus chain LA [auth B]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain FA [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain FA [auth D] mmCIF format, chain HA [auth F] mmCIF format, chain FA [auth D]	FA [auth D], HA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain FA [auth D] Focus chain HA [auth F] Interactions & Density Focus chain FA [auth D] Focus chain HA [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain IA [auth F] SDF format, chain GA [auth D] SDF format, chain EA [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain IA [auth F] MOL2 format, chain GA [auth D] MOL2 format, chain EA [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain IA [auth F] mmCIF format, chain GA [auth D] mmCIF format, chain EA [auth A]	EA [auth A], GA [auth D], IA [auth F], KA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GA [auth D] Focus chain IA [auth F] Focus chain KA [auth C] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth D] Focus chain IA [auth F] Focus chain KA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.03 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Zhang, Z.

Maharjan, R.

Tringides, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-08-06
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9BYK | pdb_00009byk

Cryo-EM structure of ATP synthase E state

Literature

Cryo-EM structure of ATP synthase E state

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 4

UniProt

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Entity ID: 5

UniProt

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Entity ID: 6

UniProt

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Entity ID: 7

UniProt

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Entity ID: 8

UniProt

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Entity ID: 9

UniProt

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Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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Entity ID: 13

UniProt

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Entity ID: 14

UniProt

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Entity ID: 15

UniProt

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Sequence Annotations

Entity ID: 16

UniProt

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Sequence Annotations

Entity ID: 17

Entity ID: 18

UniProt

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History