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

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Basic information

Entry
Database: PDB / ID: 6tdz
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring, rotational state 2
Components
  • (subunit c) x 2
  • inhibitor of F1 (IF1)
  • oligomycin sensitivity conferring protein (OSCP)
  • p18
  • subunit alpha
  • subunit beta
  • subunit d
  • subunit delta
  • subunit epsilon
  • subunit gamma
KeywordsMEMBRANE PROTEIN / mitochondria / ATP synthase
Function / homology
Function and homology information


F1F0 ATP synthase subunit C / F1FO ATP Synthase / Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold ...F1F0 ATP synthase subunit C / F1FO ATP Synthase / Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 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

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
M: oligomycin sensitivity conferring protein (OSCP)
h: subunit d
c: subunit c
G: subunit gamma
H: subunit delta
I: subunit epsilon
O: subunit c
P: subunit c
Q: subunit c
R: subunit c
S: subunit c
T: subunit c
U: subunit c
V: subunit c
W: subunit c
X: subunit c
B: subunit alpha
C: subunit alpha
A: subunit alpha
E: subunit beta
F: subunit beta
D: subunit beta
K: p18
L: p18
J: p18
N: inhibitor of F1 (IF1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)696,89037
Polymers693,96026
Non-polymers2,93011
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area119860 Å2
ΔGint-851 kcal/mol
Surface area185150 Å2
MethodPISA

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Components

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Protein , 11 types, 26 molecules MhcGHIOPQRSTUVWXBCAEFDKLJN

#1: Protein oligomycin sensitivity conferring protein (OSCP)


Mass: 29564.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#2: Protein subunit d


Mass: 53928.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#3: Protein subunit c


Mass: 18833.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#4: Protein subunit gamma


Mass: 35110.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: Protein subunit delta


Mass: 19559.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#6: Protein subunit epsilon


Mass: 8751.981 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#7: Protein
subunit c


Mass: 10820.831 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#8: Protein subunit alpha


Mass: 61897.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#9: Protein subunit beta


Mass: 53213.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#10: Protein p18


Mass: 20995.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein inhibitor of F1 (IF1)


Mass: 11687.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Non-polymers , 4 types, 11 molecules

#12: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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
#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#14: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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
#15: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE / Triton X-100


Mass: 352.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM

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Details

Has ligand of interestY

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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-#11 / 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 FIELDBright-field microscopy / 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: C1 (asymmetric)
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122085 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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