9VPB | pdb_00009vpb

Cryo-EM structure of the IF1 bound bovine F-ATP synthase planar dimer

PDB DOI: https://doi.org/10.2210/pdb9VPB/pdb
EM Map EMD-65237: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2025-07-03 Released: 2026-07-01
Deposition Author(s): Nakano, A., Jiko, C., Yamashita, E., Yokoyama, K., Gerle, C.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A planar dimer of bovine ATP synthase

Jiko, C., Nakano, A., Teshirogi, Y., Yamashita, E., Kurisu, G., Standley, D., Terada, T., Mitsuoka, K., Yokoyama, K., Gerle, C.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.07.21.665874

Macromolecule Content

Total Structure Weight: 1,367.65 kDa
Atom Count: 49,792
Modeled Residue Count: 10,134
Deposited Residue Count: 12,610
Unique protein chains: 16

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit 8	A [auth 8], C [auth A8]	66	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P03929 (Bos taurus) Explore P03929 Go to UniProtKB: P03929
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03929
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	B [auth A] D [auth AA] DA [auth B] E [auth AB] EA [auth C] B [auth A], D [auth AA], DA [auth B], E [auth AB], EA [auth C], F [auth AC]	553	Bos taurus	Mutation(s): 0
UniProt
Find proteins for F1MLB8 (Bos taurus) Explore F1MLB8 Go to UniProtKB: F1MLB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1MLB8
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex catalytic subunit beta, mitochondrial	FA [auth D] G [auth AD] GA [auth E] H [auth AE] HA [auth F] FA [auth D], G [auth AD], GA [auth E], H [auth AE], HA [auth F], I [auth AF]	528	Bos taurus	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for P00829 (Bos taurus) Explore P00829 Go to UniProtKB: P00829
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00829
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex subunit gamma, mitochondrial	IA [auth G], J [auth AG]	298	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05631 (Bos taurus) Explore P05631 Go to UniProtKB: P05631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05631
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex subunit delta, mitochondrial	JA [auth H], K [auth AH]	168	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05630 (Bos taurus) Explore P05630 Go to UniProtKB: P05630
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UniProt Group	P05630
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(1) complex subunit epsilon, mitochondrial	KA [auth I], L [auth AI]	51	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P05632 (Bos taurus) Explore P05632 Go to UniProtKB: P05632
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UniProt Group	P05632
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase inhibitor, mitochondrial	LA [auth J], M [auth AJ]	109	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P01096 (Bos taurus) Explore P01096 Go to UniProtKB: P01096
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UniProt Group	P01096
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit C2, mitochondrial	MA [auth K] N [auth AK] NA [auth L] O [auth AL] OA [auth M] MA [auth K], N [auth AK], NA [auth L], O [auth AL], OA [auth M], P [auth AM], PA [auth N], Q [auth AN], QA [auth O], R [auth AO], RA [auth P], S [auth AP], SA [auth Q], T [auth AQ], TA [auth R], U [auth AR]	143	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P07926 (Bos taurus) Explore P07926 Go to UniProtKB: P07926
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07926
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit OSCP, mitochondrial	UA [auth S], V [auth AS]	213	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P13621 (Bos taurus) Explore P13621 Go to UniProtKB: P13621
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13621
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit a	VA [auth a], W [auth Aa]	226	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00847 (Bos taurus) Explore P00847 Go to UniProtKB: P00847
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UniProt Group	P00847
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit b, mitochondrial	WA [auth b], X [auth Ab]	256	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P13619 (Bos taurus) Explore P13619 Go to UniProtKB: P13619
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13619
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit d, mitochondrial	XA [auth d], Y [auth Ad]	161	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P13620 (Bos taurus) Explore P13620 Go to UniProtKB: P13620
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13620
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit e, mitochondrial	YA [auth e], Z [auth Ae]	71	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q00361 (Bos taurus) Explore Q00361 Go to UniProtKB: Q00361
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UniProt Group	Q00361
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit f, mitochondrial	AA [auth Af], ZA [auth f]	88	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q28851 (Bos taurus) Explore Q28851 Go to UniProtKB: Q28851
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UniProt Group	Q28851
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit g, mitochondrial	AB [auth g], BA [auth Ag]	103	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q28852 (Bos taurus) Explore Q28852 Go to UniProtKB: Q28852
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UniProt Group	Q28852
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit F6, mitochondrial	BB [auth h], CA [auth Ah]	108	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02721 (Bos taurus) Explore P02721 Go to UniProtKB: P02721
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UniProt Group	P02721
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Reference Sequence