9PEW | pdb_00009pew

Porcine ATP synthase with inhibitory protein IF1, DP-state

PDB DOI: https://doi.org/10.2210/pdb9PEW/pdb
EM Map EMD-71580: EMDB EMDataResource

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

Deposited: 2025-07-02 Released: 2026-08-19
Deposition Author(s): Mnatsakanyan, N., Mello, J.F.R., Palles, C.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: integrative
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Porcine ATP synthase with inhibitory protein IF1, DP-state

Mnatsakanyan, N., Mello, J.F.R., Palles, C.

To be published.

Macromolecule Content

Total Structure Weight: 555.19 kDa
Atom Count: 38,695
Modeled Residue Count: 5,049
Deposited Residue Count: 5,082
Unique protein chains: 16

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase lipid-binding protein	A [auth 1] B [auth 2] C [auth 3] D [auth 4] E [auth 5] A [auth 1], B [auth 2], C [auth 3], D [auth 4], E [auth 5], F [auth 6], G [auth 7], H [auth 8]	73	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q4VT52 (Sus scrofa) Explore Q4VT52 Go to UniProtKB: Q4VT52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4VT52
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex subunit alpha, mitochondrial	I [auth A], J [auth B], K [auth C]	508	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P80021 (Sus scrofa) Explore P80021 Go to UniProtKB: P80021
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80021
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	L [auth D], M [auth E], N [auth F]	470	Sus scrofa	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for A0A481D232 (Sus scrofa) Explore A0A481D232 Go to UniProtKB: A0A481D232
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A481D232
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	O [auth G]	272	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1SNA2 (Sus scrofa) Explore A0A8D1SNA2 Go to UniProtKB: A0A8D1SNA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1SNA2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex subunit delta, mitochondrial	P [auth H]	132	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	Q [auth I]	47	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0X6E8 (Sus scrofa) Explore A0A8D0X6E8 Go to UniProtKB: A0A8D0X6E8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D0X6E8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase inhibitor, mitochondrial	R [auth J]	53	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 subunit b	S [auth K]	191	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TA12 (Sus scrofa) Explore A0A4X1TA12 Go to UniProtKB: A0A4X1TA12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1TA12
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit F6, mitochondrial	T [auth L]	68	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit d, mitochondrial	U [auth M]	147	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1TS79 (Sus scrofa) Explore A0A8D1TS79 Go to UniProtKB: A0A8D1TS79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1TS79
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	V [auth N]	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 peripheral stalk subunit OSCP, mitochondrial	W [auth O]	187	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q2EN81 (Sus scrofa) Explore Q2EN81 Go to UniProtKB: Q2EN81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2EN81
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit 8	X [auth Q]	22	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: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit f, mitochondrial	Y [auth R]	84	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
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Reference Sequence

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit g, mitochondrial	Z [auth S]	80	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: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit e, mitochondrial	AA [auth T]	55	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
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 F] SDF format, chain FA [auth C] SDF format, chain DA [auth B] SDF format, chain BA [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth A]	BA [auth A], DA [auth B], FA [auth C], LA [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth A] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain LA [auth F] Interactions & Density Focus chain BA [auth A] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain LA [auth F]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain HA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain HA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain HA [auth D]	HA [auth D], JA [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain HA [auth D] Focus chain JA [auth E] Interactions & Density Focus chain HA [auth D] Focus chain JA [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain KA [auth F] SDF format, chain IA [auth D] SDF format, chain GA [auth C] SDF format, chain EA [auth B] SDF format, chain CA [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain IA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain CA [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain IA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain CA [auth A]	CA [auth A], EA [auth B], GA [auth C], IA [auth D], KA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth F] Interactions & Density Focus chain CA [auth A] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Mnatsakanyan, N.

Mello, J.F.R.

Palles, C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	RF1AG072484
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R21NS137275

Revision History (Full details and data files)

Version 1.0: 2026-08-19
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.

9PEW | pdb_00009pew

Porcine ATP synthase with inhibitory protein IF1, DP-state

Literature

Porcine ATP synthase with inhibitory protein IF1, DP-state

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)