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- PDB-6tdv: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -

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Basic information

Entry
Database: PDB / ID: 6tdv
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane region
Components
  • ATPEG1
  • ATPEG2
  • ATPEG3
  • ATPEG4
  • ATPEG5
  • ATPEG6
  • ATPEG7
  • ATPEG8
  • ATPTB1
  • ATPTB12
  • ATPTB3
  • ATPTB6
  • subunit 8
  • subunit a
  • subunit b
  • subunit d
  • subunit f
  • subunit i/j
  • subunit k
KeywordsMEMBRANE PROTEIN / mitochondria / ATP synthase
Function / homologyCARDIOLIPIN / Chem-LPP
Function and homology information
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMuhleip, A. / Amunts, A.
CitationJournal: Elife / Year: 2019
Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts /
Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids.
History
DepositionNov 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-10468
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Structure viewerMolecule:
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Assembly

Deposited unit
A: ATPTB1
B: ATPTB3
D: ATPTB6
E: ATPTB12
F: subunit a
G: subunit b
H: subunit d
I: subunit f
J: subunit i/j
K: subunit k
L: subunit 8
M: ATPEG1
N: ATPEG2
O: ATPEG3
P: ATPEG4
Q: ATPEG5
R: ATPEG6
S: ATPEG7
T: ATPEG8
a: ATPTB1
b: ATPTB3
d: ATPTB6
e: ATPTB12
f: subunit a
g: subunit b
h: subunit d
i: subunit f
j: subunit i/j
k: subunit k
l: subunit 8
m: ATPEG1
n: ATPEG2
o: ATPEG3
p: ATPEG4
q: ATPEG5
r: ATPEG6
s: ATPEG7
t: ATPEG8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)787,99399
Polymers733,88038
Non-polymers54,11361
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 19 types, 38 molecules AaBbDdEeFfGgHhIiJjKkLlMmNnOoPp...

#1: Protein ATPTB1


Mass: 56026.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#2: Protein ATPTB3


Mass: 35175.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#3: Protein ATPTB6


Mass: 21737.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#4: Protein ATPTB12


Mass: 11432.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: Protein subunit a


Mass: 32666.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#6: Protein subunit b


Mass: 12673.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#7: Protein subunit d


Mass: 53928.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#8: Protein subunit f


Mass: 11193.877 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#9: Protein subunit i/j


Mass: 12529.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#10: Protein subunit k


Mass: 12739.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein subunit 8


Mass: 7011.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#12: Protein ATPEG1


Mass: 19738.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#13: Protein ATPEG2


Mass: 16210.519 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#14: Protein ATPEG3


Mass: 13807.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#15: Protein ATPEG4


Mass: 13703.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#16: Protein ATPEG5


Mass: 10825.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#17: Protein ATPEG6


Mass: 9236.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#18: Protein ATPEG7


Mass: 8861.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#19: Protein ATPEG8


Mass: 7441.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Sugars , 1 types, 8 molecules

#21: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 53 molecules

#20: 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.: 25 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#22: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: Euglena gracilis mitochondrial ATP synthase dimer / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Euglena gracilis (euglena)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 seconds blot

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 36.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 9045
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
2EPUimage acquisition
4RELIONCTF correction
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 555269
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150242 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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