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

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Basic information

Entry
Database: PDB / ID: 6tdu
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, full dimer, rotational states 1
Components
  • (ATP synthase subunit ...) x 13
  • ATPEG1
  • ATPEG2
  • ATPEG3
  • ATPEG4
  • ATPEG5
  • ATPEG6
  • ATPEG7
  • ATPEG8
  • ATPTB1
  • ATPTB12
  • ATPTB3
  • ATPTB4
  • ATPTB6
  • inhibitor of F1 (IF1)
  • oligomycin sensitivity conferring protein (OSCP)
  • p18
KeywordsMEMBRANE PROTEIN / mitochondria / ATP synthase
Function / homologyADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / Chem-LPP
Function and homology information
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 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 1.1Oct 23, 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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Assembly

Deposited unit
A: ATPTB1
D: ATPTB6
E: ATPTB12
F: ATP synthase subunit a
G: ATP synthase subunit b
H: ATP synthase subunit d
I: ATP synthase subunit f
J: ATP synthase subunit i/j
K: ATP synthase subunit k
L: ATP synthase subunit 8
M: ATPEG1
N: ATPEG2
O: ATPEG3
P: ATPEG4
Q: ATPEG5
R: ATPEG6
S: ATPEG7
T: ATPEG8
a: ATPTB1
d: ATPTB6
e: ATPTB12
f: ATP synthase subunit a
g: ATP synthase subunit b
h: ATP synthase subunit d
i: ATP synthase subunit f
j: ATP synthase subunit i/j
k: ATP synthase subunit k
l: ATP synthase subunit 8
m: ATPEG1
n: ATPEG2
o: ATPEG3
p: ATPEG4
q: ATPEG5
r: ATPEG6
s: ATPEG7
t: ATPEG8
AA: ATP synthase subunit alpha
AB: ATP synthase subunit alpha
AC: ATP synthase subunit alpha
AD: ATP synthase subunit beta
AE: ATP synthase subunit beta
AF: ATP synthase subunit beta
AG: ATP synthase subunit gamma
AH: ATP synthase subunit delta
AI: ATP synthase subunit epsilon
AJ: p18
AK: p18
AL: p18
AM: oligomycin sensitivity conferring protein (OSCP)
AN: inhibitor of F1 (IF1)
AO: ATP synthase subunit c
AP: ATP synthase subunit c
AQ: ATP synthase subunit c
AR: ATP synthase subunit c
AS: ATP synthase subunit c
AT: ATP synthase subunit c
AU: ATP synthase subunit c
AV: ATP synthase subunit c
AW: ATP synthase subunit c
AX: ATP synthase subunit c
B: ATPTB3
C: ATPTB4
BA: ATP synthase subunit alpha
BB: ATP synthase subunit alpha
BC: ATP synthase subunit alpha
BD: ATP synthase subunit beta
BE: ATP synthase subunit beta
BF: ATP synthase subunit beta
BG: ATP synthase subunit gamma
BH: ATP synthase subunit delta
BI: ATP synthase subunit epsilon
BJ: p18
BK: p18
BL: p18
BM: oligomycin sensitivity conferring protein (OSCP)
BN: inhibitor of F1 (IF1)
BO: ATP synthase subunit c
BP: ATP synthase subunit c
BQ: ATP synthase subunit c
BR: ATP synthase subunit c
BS: ATP synthase subunit c
BT: ATP synthase subunit c
BU: ATP synthase subunit c
BV: ATP synthase subunit c
BW: ATP synthase subunit c
BX: ATP synthase subunit c
b: ATPTB3
c: ATPTB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,078,585171
Polymers2,018,61288
Non-polymers59,97383
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 , 16 types, 36 molecules AaDdEeMmNnOoPpQqRrSsTtAJAKALBJBKBLAMBM...

#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 ATPTB6


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


Mass: 11432.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein ATPEG1


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


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


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


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


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


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


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


Mass: 7441.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#24: Protein
p18


Mass: 20995.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#25: Protein oligomycin sensitivity conferring protein (OSCP)


Mass: 29564.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#26: Protein inhibitor of F1 (IF1)


Mass: 11687.415 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#28: Protein ATPTB3


Mass: 35175.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#29: Protein ATPTB4


Mass: 18833.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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ATP synthase subunit ... , 13 types, 52 molecules FfGgHhIiJjKkLlAAABACBABBBCADAEAFBDBEBFAGBGAHBH...

#4: Protein ATP synthase subunit a


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


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


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


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


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


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


Mass: 7011.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#19: Protein
ATP synthase subunit alpha


Mass: 61897.199 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#20: Protein
ATP synthase subunit beta


Mass: 53991.066 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#21: Protein ATP synthase subunit gamma


Mass: 35110.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#22: Protein ATP synthase subunit delta


Mass: 19559.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#23: Protein ATP synthase subunit epsilon


Mass: 8751.981 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#27: Protein
ATP synthase subunit c


Mass: 10820.831 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Sugars , 1 types, 8 molecules

#31: 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 , 6 types, 75 molecules

#30: 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
#32: 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
#33: 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.: 18 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#34: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#35: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#36: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*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-#29 / 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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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
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: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27232 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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