9B3J | pdb_00009b3j

Artemia franciscana ATP synthase state 2 (composite structure), pH 8.0

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Artemia franciscana
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-03-19 Released: 2025-03-26 
  • Deposition Author(s): Mnatsakanyan, N., Mello, J.F.R.
  • 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: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: integrative
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.

Kumar, A.da Fonseca Rezende E Mello, J.Wu, Y.Morris, D.Mezghani, I.Smith, E.Rombauts, S.Bossier, P.Krahn, J.Sigworth, F.J.Mnatsakanyan, N.

(2025) Cell Death Differ 32: 1518-1535

  • DOI: https://doi.org/10.1038/s41418-025-01476-w
  • Primary Citation of Related Structures:  
    9B0X, 9B3J, 9BPG

  • PubMed Abstract: 

    Mammalian mitochondria undergo Ca 2+ -induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial inner membranes. Ca 2+ -induced prolonged openings of mPTP under certain pathological conditions result in mitochondrial swelling and rupture of the outer membrane, leading to mitochondrial dysfunction and cell death. While the exact molecular composition and structure of mPTP remain unknown, mammalian ATP synthase was reported to form voltage and Ca 2+ -activated leak channels involved in mPT. Unlike in mammals, mitochondria of the crustacean Artemia franciscana have the ability to accumulate large amounts of Ca 2+ without undergoing the mPT. Here, we performed structural and functional analysis of A. franciscana ATP synthase to study the molecular mechanism of mPTP inhibition in this organism. We found that the channel formed by the A. franciscana ATP synthase dwells predominantly in its inactive state and is insensitive to Ca 2+ , in contrast to porcine heart ATP synthase. Single-particle cryo-electron microscopy (cryo-EM) analysis revealed distinct structural features in A. franciscana ATP synthase compared with mammals. The stronger density of the e-subunit C-terminal region and its enhanced interaction with the c-ring were found in A. franciscana ATP synthase. These data suggest an inactivation mechanism of the ATP synthase leak channel and its possible contribution to the lack of mPT in this organism.


  • Organizational Affiliation
    • Department of Cell and Biological Systems, Penn State College of Medicine, Hershey, PA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c128Artemia franciscanaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaI [auth A],
J [auth B],
K [auth C]
551Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HWD9 (Artemia franciscana)
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UniProt GroupA0AA88HWD9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaL [auth D],
M [auth E],
N [auth F]
524Artemia franciscanaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaO [auth G]290Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HFG7 (Artemia franciscana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaP [auth H]169Artemia franciscanaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilonQ [auth I]66Artemia franciscanaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bR [auth K]265Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88H718 (Artemia franciscana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase coupling factor 6, F6S [auth L]99Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HKM7 (Artemia franciscana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit dT [auth M]219Artemia franciscanaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aU [auth N]219Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q37708 (Artemia franciscana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit OSCPV [auth O]207Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HW36 (Artemia franciscana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 6.8PLW [auth P]44Artemia franciscanaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8X [auth Q]53Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q37707 (Artemia franciscana)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit fY [auth R]119Artemia franciscanaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gZ [auth S]103Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HPA7 (Artemia franciscana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit eAA [auth T]84Artemia franciscanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA88HBT7 (Artemia franciscana)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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JA [auth R],
KA [auth S]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
ATP (Subject of Investigation/LOI)
Query on ATP

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BA [auth A],
DA [auth B],
FA [auth C],
HA [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

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CA [auth A],
EA [auth B],
GA [auth C],
IA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesRF1AG072484
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR21NS137275

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references