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- PDB-9b0x: Artemia franciscana ATP synthase state 2 (composite structure), pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 9b0x
TitleArtemia franciscana ATP synthase state 2 (composite structure), pH 7.0
Components(ATP synthase ...) x 17
KeywordsMEMBRANE PROTEIN / ATP synthesis / Complex V / mitochondria / oxidative-phosphorylation
Function / homology
Function and homology information


ATP biosynthetic process / proton-transporting ATP synthase complex / : / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / ATP synthase protein 8 / ATP synthase subunit a
Similarity search - Component
Biological speciesArtemia franciscana (crustacean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMnatsakanyan, N. / Mello, J.F.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG072484 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS137275 United States
CitationJournal: Cell Death Differ / Year: 2025
Title: Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.
Authors: Amrendra Kumar / Juliana da Fonseca Rezende E Mello / Yangyu Wu / Daniel Morris / Ikram Mezghani / Erin Smith / Stephane Rombauts / Peter Bossier / Juno Krahn / Fred J Sigworth / Nelli Mnatsakanyan /
Abstract: Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial ...Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial inner membranes. Ca-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-activated leak channels involved in mPT. Unlike in mammals, mitochondria of the crustacean Artemia franciscana have the ability to accumulate large amounts of Ca 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, 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.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: ATP synthase subunit c
2: ATP synthase subunit c
3: ATP synthase subunit c
4: ATP synthase subunit c
5: ATP synthase subunit c
6: ATP synthase subunit c
7: ATP synthase subunit c
8: ATP synthase subunit c
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
J: ATP synthase inhibitory factor 1, IF1
K: ATP synthase subunit b
L: ATP synthase coupling factor 6, F6
M: ATP synthase subunit d
N: ATP synthase subunit a
O: ATP synthase subunit OSCP
P: ATP synthase subunit 6.8PL
Q: ATP synthase protein 8
R: ATP synthase subunit f
S: ATP synthase subunit g
T: ATP synthase subunit e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)685,36440
Polymers679,85928
Non-polymers5,50612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ATP synthase ... , 17 types, 28 molecules 12345678ABCDEFGHIJKLMNOPQRST

#1: Protein
ATP synthase subunit c


Mass: 13250.408 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#2: Protein ATP synthase subunit alpha


Mass: 59706.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#3: Protein ATP synthase subunit beta


Mass: 55884.770 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#4: Protein ATP synthase subunit gamma


Mass: 31976.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#5: Protein ATP synthase subunit delta


Mass: 17565.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#6: Protein ATP synthase subunit epsilon


Mass: 7464.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#7: Protein ATP synthase inhibitory factor 1, IF1


Mass: 11974.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#8: Protein ATP synthase subunit b


Mass: 29944.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#9: Protein ATP synthase coupling factor 6, F6


Mass: 11140.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#10: Protein ATP synthase subunit d


Mass: 25422.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#11: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24422.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean) / References: UniProt: Q37708
#12: Protein ATP synthase subunit OSCP


Mass: 22563.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#13: Protein/peptide ATP synthase subunit 6.8PL


Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#14: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 6351.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean) / References: UniProt: Q37707
#15: Protein ATP synthase subunit f


Mass: 13697.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#16: Protein ATP synthase subunit g


Mass: 11236.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)
#17: Protein ATP synthase subunit e


Mass: 9557.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean)

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Non-polymers , 4 types, 12 molecules

#18: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#19: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#21: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial ATP synthase / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Source (natural)Organism: Artemia franciscana (crustacean)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 15.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232736 / Symmetry type: POINT
Atomic model buildingDetails: Genome annotation and AlphaFold / Source name: Other / Type: integrative model

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