ISDA

Deposition Date 2019-01-11

Release Date 2019-06-26

Last Version Date 2024-03-27

Entry Detail

PDB ID:

6J5I

Keywords:

MEMBRANE PROTEIN

Title:

Cryo-EM structure of the mammalian DP-state ATP synthase

Biological Source:

Source Organism:

Sus scrofa (Taxon ID: 9823)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.34 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase protein 8
Gene (Uniprot):MT-ATP8
Chain IDs:T (auth: 8)
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q35914 Pfam ID:PF00895

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit alpha, mitochondrial
Gene (Uniprot):ATP5F1A
Chain IDs:A, B, C
Chain Length:226
Number of Molecules:3
Biological Source:Sus scrofa

UniProt ID:P80021 Pfam ID:PF02874, PF00006, PF00306

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit beta
Gene (Uniprot):ATP5F1B
Chain IDs:D, E, F
Chain Length:480
Number of Molecules:3
Biological Source:Sus scrofa

UniProt ID:K7GLT8 Pfam ID:PF02874, PF00006, PF22919

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit gamma
Chain IDs:H (auth: G)
Chain Length:272
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit delta, mitochondrial
Gene (Uniprot):ATP5F1D
Chain IDs:I (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A286ZYL7 Pfam ID:PF02823, PF21335

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase F1 subunit epsilon
Gene (Uniprot):ATP5E
Chain IDs:J (auth: I)
Chain Length:48
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A5GFX4 Pfam ID:PF04627

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATPase inhibitor, mitochondrial
Gene (Uniprot):ATP5IF1
Chain IDs:G (auth: J)
Chain Length:83
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29307 Pfam ID:PF04568

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial H+ transporting ATP synthase subunit c isoform 1
Chain IDs:V (auth: K), W (auth: L), X (auth: M), Y (auth: N), Z (auth: O), AA (auth: P), BA (auth: Q), CA (auth: R)
Chain Length:72
Number of Molecules:8
Biological Source:Sus scrofa

UniProt ID:Q4VT52 Pfam ID:PF00137

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit O, mitochondrial
Gene (Uniprot):ATP5PO
Chain IDs:K (auth: S)
Chain Length:187
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q2EN81 Pfam ID:PF00213

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit a
Gene (Uniprot):MT-ATP6
Chain IDs:U (auth: a)
Chain Length:226
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q35915 Pfam ID:PF00119

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase peripheral stalk-membrane subunit b
Chain IDs:L (auth: b)
Chain Length:209
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A8D0MI69 Pfam ID:PF05405

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase-coupling factor 6, mitochondrial
Gene (Uniprot):ATP5PF
Chain IDs:M (auth: c)
Chain Length:70
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P13618 Pfam ID:PF05511

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit d, mitochondrial
Gene (Uniprot):ATP5PD
Chain IDs:N (auth: d)
Chain Length:480
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287B4I0 Pfam ID:PF05873

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit e
Chain IDs:O (auth: e)
Chain Length:480
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit f, mitochondrial
Gene (Uniprot):ATP5MF
Chain IDs:P (auth: f)
Chain Length:87
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q95339 Pfam ID:PF10206

Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit g
Chain IDs:Q (auth: g)
Chain Length:272
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP synthase membrane subunit DAPIT
Chain IDs:R (auth: i)
Chain Length:48
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TQQ5 Pfam ID:PF14960

Polymer Type:polypeptide(L)
Molecule:subunit k analog
Chain IDs:S (auth: k)
Chain Length:72
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:ATP synthase membrane subunit 6.8PL
Chain IDs:DA (auth: u)
Chain Length:42
Number of Molecules:1
Biological Source:Sus scrofa

Ligand Molecules

ADP

ATP

Primary Citation

Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1.

Gu, J, Zhang, L, Zong, S, Guo, R, Liu, T, Yi, J, Wang, P, Zhuo, W, Yang, M.Show

Science 364 1068 1075 (2019)

PMID: 31197009 DOI: 10.1126/science.aaw4852

Abstact

The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.

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Protein

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Disease

Primary Citation of related structures