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- PDB-6tmg: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

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Entry
Database: PDB / ID: 6tmg
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, membrane region model
Components
  • ATPTG1
  • ATPTG10
  • ATPTG11
  • ATPTG12
  • ATPTG13
  • ATPTG14
  • ATPTG15
  • ATPTG16
  • ATPTG17
  • ATPTG2
  • ATPTG3
  • ATPTG4
  • ATPTG5
  • ATPTG6
  • ATPTG7
  • ATPTG8
  • ATPTG9
  • subunit 8
  • subunit a
  • subunit b
  • subunit d
  • subunit f
  • subunit i/j
  • subunit k
KeywordsMEMBRANE PROTEIN / mitochondrial / ATP synthase / membrane region / lipids
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / mitochondrial inner membrane / electron transfer activity / heme binding / membrane / metal ion binding
Similarity search - Function
: / Domain of unknown function (DUF6828) / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c1 / Cytochrome C1 family / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Thioredoxin / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...: / Domain of unknown function (DUF6828) / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c1 / Cytochrome C1 family / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Thioredoxin / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Uncharacterized protein / Putative membrane protein / Transmembrane protein / ATPTG10-like domain-containing protein / Transmembrane protein ...CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Uncharacterized protein / Putative membrane protein / Transmembrane protein / ATPTG10-like domain-containing protein / Transmembrane protein / Uncharacterized protein / Transmembrane protein / Transmembrane protein / Uncharacterized protein / CHCH domain-containing protein / Uncharacterized protein / Transmembrane protein / Transmembrane protein / Thioredoxin domain-containing protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Uncharacterized protein / Transmembrane protein / Putative myosin heavy chain / Cytochrome c1, heme protein / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research CouncilERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology OrganizationALTF 260-2017 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Jana Ovciarikova / Alice Lacombe / Paula Fernandes / Lilach Sheiner / Alexey Amunts /
Abstract: Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has ...Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.
History
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
q: ATPTG11
i: ATPTG7
t: ATPTG14
g: ATPTG5
o: subunit k
k: subunit a
j: subunit i/j
s: ATPTG13
u: ATPTG15
h: ATPTG6
e: ATPTG3
x: ATPTG17
b: subunit b
r: ATPTG12
p: ATPTG10
v: subunit f
l: ATPTG8
c: ATPTG1
d: ATPTG2
m: subunit 8
n: ATPTG9
f: ATPTG4
w: ATPTG16
a: subunit d
Q: ATPTG11
I: ATPTG7
T: ATPTG14
G: ATPTG5
O: subunit k
K: subunit a
J: subunit i/j
S: ATPTG13
U: ATPTG15
H: ATPTG6
E: ATPTG3
X: ATPTG17
B: subunit b
R: ATPTG12
P: ATPTG10
V: subunit f
L: ATPTG8
C: ATPTG1
D: ATPTG2
M: subunit 8
N: ATPTG9
F: ATPTG4
W: ATPTG16
A: subunit d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,21792
Polymers1,220,48048
Non-polymers42,73744
Water0
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 , 24 types, 48 molecules qQiItTgGoOkKjJsSuUhHeExXbBrRpP...

#1: Protein ATPTG11


Mass: 15425.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YPS4
#2: Protein ATPTG7


Mass: 26866.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7VXW3
#3: Protein ATPTG14


Mass: 14424.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLH9
#4: Protein ATPTG5


Mass: 28162.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7WD71
#5: Protein subunit k


Mass: 17963.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YTD7
#6: Protein subunit a


Mass: 24562.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YSI9
#7: Protein subunit i/j


Mass: 26600.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UQ82
#8: Protein ATPTG13


Mass: 14923.235 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLN4
#9: Protein ATPTG15


Mass: 13871.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YRP0
#10: Protein ATPTG6


Mass: 27477.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YL08
#11: Protein ATPTG3


Mass: 35159.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YLR0
#12: Protein ATPTG17


Mass: 9486.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W180
#13: Protein subunit b


Mass: 64811.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7V2T0
#14: Protein ATPTG12


Mass: 15400.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YKF7
#15: Protein ATPTG10


Mass: 15165.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YMA7
#16: Protein subunit f


Mass: 13029.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UQT7
#17: Protein ATPTG8


Mass: 23365.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W7F1
#18: Protein ATPTG1


Mass: 46025.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7W9J5
#19: Protein ATPTG2


Mass: 35238.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YV76
#20: Protein subunit 8


Mass: 22344.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YPQ4
#21: Protein ATPTG9


Mass: 18426.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: A0A125YUZ2
#22: Protein ATPTG4


Mass: 28557.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7UVZ7
#23: Protein ATPTG16


Mass: 11587.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7VTI0
#24: Protein subunit d


Mass: 61362.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1 / References: UniProt: S7V493

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Sugars , 1 types, 14 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 30 molecules

#25: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#27: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 749.073 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H83NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*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: Mitochondrial ATP synthase dimer, membrane region / Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 0.90 MDa / Experimental value: NO
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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: 165000 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 4860
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4GctfCTF correction
9PHENIX1.17rc2-3612model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101505 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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