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- PDB-9bpg: Artemia franciscana ATP synthase FO domain, state 1, pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 9bpg
TitleArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Components
  • (ATP synthase subunit ...) x 11
  • ATP synthase protein 8
KeywordsMEMBRANE PROTEIN / ATP synthesis / Complex V / mitochondria / oxidative-phosphorylation
Function / homology
Function and homology information


ATP biosynthetic process / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / : / : / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase
Similarity search - Domain/homology
CARDIOLIPIN / ATP synthase subunit e, mitochondrial / ATP synthase subunit gamma / ATP synthase subunit / ATP synthase protein 8 / ATP synthase subunit a
Similarity search - Component
Biological speciesArtemia franciscana (crustacean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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
DepositionMay 7, 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

Downloads & links

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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
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
K: ATP synthase subunit b
M: ATP synthase subunit d
N: ATP synthase subunit a
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)290,33421
Polymers287,40619
Non-polymers2,9282
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 subunit ... , 11 types, 18 molecules 12345678GHIKMNPRST

#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 gamma


Mass: 31976.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artemia franciscana (crustacean) / References: UniProt: A0AA88HFG7
#3: 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)
#4: 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)
#5: 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)
#6: 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)
#7: 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
#8: 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)
#10: 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)
#11: 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) / References: UniProt: A0AA88HPA7
#12: 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) / References: UniProt: A0AA88HBT7

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Protein / Non-polymers , 2 types, 3 molecules Q

#13: 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
#9: 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

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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-#12 / Source: NATURAL
Source (natural)Organism: Artemia franciscana (crustacean)
Buffer solutionpH: 7
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 software
IDNameCategory
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 673185 / Symmetry type: POINT
Atomic model buildingDetails: Genome annotation and Alpha fold / Source name: Other / Type: integrative model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414015
ELECTRON MICROSCOPYf_angle_d0.60218884
ELECTRON MICROSCOPYf_dihedral_angle_d13.3725075
ELECTRON MICROSCOPYf_chiral_restr0.0432108
ELECTRON MICROSCOPYf_plane_restr0.0052370

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