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- PDB-8apg: rotational state 2b of the Trypanosoma brucei mitochondrial ATP s... -

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Entry
Database: PDB / ID: 8apg
Titlerotational state 2b of the Trypanosoma brucei mitochondrial ATP synthase dimer
Components
  • (ATP synthase subunit ...) x 5
  • ATP synthase gamma subunit
  • ATP synthase, epsilon chain, putative
  • ATPEG3
  • ATPEG4
  • ATPTB1
  • ATPTB11
  • ATPTB12
  • ATPTB3
  • ATPTB4
  • ATPTB6
  • ATPase subunit 9, putative
  • OSCP
  • 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


H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / : / : / : / : ...H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / membrane / cytoplasm
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain ...ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, beta subunit / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / URIDINE 5'-TRIPHOSPHATE / ATP synthase subunit gamma, mitochondrial / Uncharacterized protein / T. brucei spp.-specific protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / URIDINE 5'-TRIPHOSPHATE / ATP synthase subunit gamma, mitochondrial / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / Transmembrane protein / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit p18, mitochondrial / ATP synthase subunit a / Uncharacterized protein / Uncharacterized protein / ATP synthase delta chain, mitochondrial / ATPase subunit 9, putative / Letm1 RBD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / ATP synthase, epsilon chain, putative / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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

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Assembly

Deposited unit
L: subunit-e
M: subunit-g
a: ATP synthase subunit a
c: subunit-8
d: subunit-d
e: ATPTB1
f: subunit-f
g: ATPTB3
h: ATPTB4
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
H1: ATP synthase, epsilon chain, putative
I1: ATP synthase subunit epsilon, mitochondrial
J1: ATP synthase subunit p18, mitochondrial
K1: ATP synthase subunit p18, mitochondrial
L1: ATP synthase subunit p18, mitochondrial
M1: OSCP
O1: ATPase subunit 9, putative
P1: ATPase subunit 9, putative
Q1: ATPase subunit 9, putative
R1: ATPase subunit 9, putative
S1: ATPase subunit 9, putative
T1: ATPase subunit 9, putative
U1: ATPase subunit 9, putative
V1: ATPase subunit 9, putative
W1: ATPase subunit 9, putative
X1: ATPase subunit 9, putative
G1: ATP synthase gamma subunit
A1: ATP synthase subunit alpha, mitochondrial
B1: ATP synthase subunit alpha, mitochondrial
C1: ATP synthase subunit alpha, mitochondrial
D1: ATP synthase subunit beta, mitochondrial
E1: ATP synthase subunit beta, mitochondrial
F1: ATP synthase subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,027,78178
Polymers995,47842
Non-polymers32,30336
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area255290 Å2
ΔGint-1932 kcal/mol
Surface area296340 Å2

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Components

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Protein , 20 types, 31 molecules LlMmcdefghijknopqrH1M1O1P1Q1R1S1T1U1V1W1X1G1

#1: 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
#2: 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
#4: Protein subunit-8


Mass: 13750.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585K5
#5: Protein subunit-d


Mass: 43379.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZW9
#6: Protein ATPTB1


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


Mass: 17182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZE2
#8: Protein ATPTB3


Mass: 27646.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6KRX7
#9: Protein ATPTB4


Mass: 17218.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q389Z3
#10: Protein subunit-i/j


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


Mass: 20307.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A5R7
#12: Protein subunit-k


Mass: 14531.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57VT0
#13: Protein ATPTB11


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


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


Mass: 12325.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZLR9
#16: Protein ATPEG3


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


Mass: 7649.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#18: Protein ATP synthase, epsilon chain, putative


Mass: 20172.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
References: UniProt: Q586H1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#21: Protein OSCP


Mass: 28869.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38AG1
#22: Protein
ATPase subunit 9, putative


Mass: 12398.870 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
References: UniProt: Q38C84, H+-transporting two-sector ATPase
#23: Protein ATP synthase gamma subunit


Mass: 34472.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
References: UniProt: A0A161CM65, H+-transporting two-sector ATPase

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ATP synthase subunit ... , 5 types, 11 molecules aI1J1K1L1A1B1C1D1E1F1

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


Mass: 28708.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P24499
#19: Protein ATP synthase subunit epsilon, mitochondrial / ATP synthase F1 subunit epsilon


Mass: 8706.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P0DPG3
#20: Protein ATP synthase subunit p18, mitochondrial / ATP synthase F1 subunit p18


Mass: 21268.279 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P0DPG4
#24: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 63574.465 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q9GS23
#25: Protein ATP synthase subunit beta, mitochondrial / ATP synthase F1 subunit beta


Mass: 55836.879 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
References: UniProt: Q9GPE9, H+-transporting two-sector ATPase

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Sugars , 1 types, 2 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 34 molecules

#26: 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.: 14 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#27: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#29: 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.: 2 / Source method: obtained synthetically / Formula: C56H92O25
#30: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#31: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#32: Chemical
ChemComp-ATP / ADENOSINE-5'-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
#33: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-ADP / ADENOSINE-5'-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

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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 from Trypanosoma brucei / Type: COMPLEX / Entity ID: #1-#25 / 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
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 FIELD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24096 / Symmetry type: POINT

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