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- PDB-8ap7: membrane region of the Trypanosoma brucei mitochondrial ATP synth... -

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Basic information

Entry
Database: PDB / ID: 8ap7
Titlemembrane region of the Trypanosoma brucei mitochondrial ATP synthase dimer
Components
  • ATP synthase subunit a
  • ATPEG3
  • ATPEG4
  • ATPTB1
  • ATPTB11
  • ATPTB12
  • ATPTB6
  • subunit-8
  • subunit-b
  • subunit-d
  • subunit-e
  • subunit-f
  • subunit-g
  • subunit-i/j
  • subunit-k
KeywordsMEMBRANE PROTEIN / ATP synthase / mitochondria
Function / homology
Function and homology information


kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion ...kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion / membrane / cytoplasm
Similarity search - Function
CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / T. brucei spp.-specific protein / Uncharacterized protein / Transmembrane protein / ATP synthase subunit a / Uncharacterized protein / Letm1 RBD domain-containing protein ...CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / T. brucei spp.-specific protein / Uncharacterized protein / Transmembrane protein / ATP synthase subunit a / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMuehleip, A. / Gahura, O. / Zikova, A. / Amunts, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2022
Title: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
Authors: Ondřej Gahura / Alexander Mühleip / Carolina Hierro-Yap / Brian Panicucci / Minal Jain / David Hollaus / Martina Slapničková / Alena Zíková / Alexey Amunts /
Abstract: Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM ...Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.
History
DepositionAug 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit a
C: subunit-8
D: subunit-d
E: ATPTB1
F: subunit-f
I: subunit-i/j
J: ATPTB6
K: subunit-k
L: subunit-e
M: subunit-g
N: ATPTB11
O: ATPTB12
P: subunit-b
Q: ATPEG3
R: ATPEG4
a: ATP synthase subunit a
c: subunit-8
d: subunit-d
e: ATPTB1
f: subunit-f
i: subunit-i/j
j: ATPTB6
k: subunit-k
l: subunit-e
m: subunit-g
n: ATPTB11
o: ATPTB12
p: subunit-b
q: ATPEG3
r: ATPEG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)622,78174
Polymers571,64330
Non-polymers51,13844
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area245750 Å2
ΔGint-1906 kcal/mol
Surface area164430 Å2

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Components

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Protein , 15 types, 30 molecules AaCcDdEeFfIiJjKkLlMmNnOoPpQqRr

#1: Protein ATP synthase subunit a / / F-ATPase protein 6


Mass: 28708.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P24499
#2: Protein subunit-8


Mass: 13750.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585K5
#3: Protein subunit-d


Mass: 43379.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZW9
#4: Protein ATPTB1


Mass: 46883.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38CI8
#5: Protein subunit-f


Mass: 17182.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZE2
#6: Protein subunit-i/j


Mass: 12661.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZM4
#7: Protein ATPTB6


Mass: 20307.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A5R7
#8: Protein subunit-k


Mass: 14531.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57VT0
#9: Protein subunit-e


Mass: 10448.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q387J1
#10: Protein subunit-g


Mass: 16092.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZJA0
#11: Protein ATPTB11


Mass: 17929.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q582T1
#12: Protein ATPTB12


Mass: 11676.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57Z84
#13: Protein subunit-b


Mass: 12325.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZLR9
#14: Protein ATPEG3


Mass: 12293.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q583U4
#15: Protein ATPEG4


Mass: 7649.776 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister427

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Sugars , 1 types, 4 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 64 molecules

#16: 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.: 24 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#18: Chemical
ChemComp-Q7G / 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside


Mass: 1165.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H92O25
#19: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#20: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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 from Trypanosoma brucei
Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 / Organelle: Mitochondrion
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingElectron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19rc4_4035: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100605 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00438912
ELECTRON MICROSCOPYf_angle_d0.45352063
ELECTRON MICROSCOPYf_dihedral_angle_d12.29715490
ELECTRON MICROSCOPYf_chiral_restr0.0355104
ELECTRON MICROSCOPYf_plane_restr0.0046210

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