8F29 image
Entry Detail
PDB ID:
8F29
EMDB ID:
Title:
Yeast ATP synthase in conformation-1 at pH 6
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-11-07
Release Date:
2024-02-07
Method Details:
Experimental Method:
Resolution:
4.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:ATP synthase subunit H, mitochondrial
Chain IDs:G (auth: 6)
Chain Length:89
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit d, mitochondrial
Chain IDs:F (auth: 7)
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase protein 8
Chain IDs:S (auth: 8)
Chain Length:41
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit alpha, mitochondrial
Chain IDs:V (auth: A), W (auth: B), X (auth: C)
Chain Length:507
Number of Molecules:3
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit beta, mitochondrial
Chain IDs:Y (auth: D), Z (auth: E), AA (auth: F)
Chain Length:473
Number of Molecules:3
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit gamma, mitochondrial
Chain IDs:B (auth: G)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit delta, mitochondrial
Chain IDs:C (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit epsilon, mitochondrial
Chain IDs:D (auth: I)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit J, mitochondrial
Chain IDs:U (auth: J)
Chain Length:37
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit 9, mitochondrial
Chain IDs:I (auth: S), J (auth: T), K, L, M, N, O, P, Q, R
Chain Length:75
Number of Molecules:10
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit f, mitochondrial
Chain IDs:H (auth: U)
Chain Length:85
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit a
Chain IDs:T (auth: X)
Chain Length:224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit 5, mitochondrial
Chain IDs:A (auth: Y)
Chain Length:187
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:ATP synthase subunit 4, mitochondrial
Chain IDs:E (auth: Z)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F 1 -F o coupling.
Nat.Struct.Mol.Biol. 31 657 666 (2024)
PMID: 38316880 DOI: 10.1038/s41594-024-01219-4

Abstact

Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at neutral or basic pH have provided details of the reaction mechanism of ATP synthesis. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported. Here we use single-particle cryo-EM to analyze the conformational ensemble of the yeast (Saccharomyces cerevisiae) ATP synthase at pH 6. Of the four conformations resolved in this study, three are reaction intermediates. In addition to canonical catalytic dwell and binding dwell structures, we identify two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations. These structures provide new insights into the catalytic mechanism of the ATP synthase and highlight elastic coupling between the catalytic and proton translocating domains.

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