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- EMDB-15562: rotor of the Trypanosoma brucei mitochondrial ATP synthase dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-15562
Titlerotor of the Trypanosoma brucei mitochondrial ATP synthase dimer
Map data
Sample
  • Organelle or cellular component: mitochondrial ATP synthase dimer from Trypanosoma brucei
    • Protein or peptide: ATP synthase gamma subunit
    • Protein or peptide: ATP synthase, epsilon chain, putative
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
    • Protein or peptide: ATPase subunit 9, putative
  • Ligand: URIDINE 5'-TRIPHOSPHATE
KeywordsATP synthase / mitochondria / MEMBRANE PROTEIN
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 / : / : / : / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane ...H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / : / : / : / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / hydrolase activity / lipid binding / mitochondrion
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATPase subunit 9, putative / ATP synthase, epsilon chain, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMuehleip A / Gahura O / Zikova A / Amunts A
Funding supportEuropean Union, 1 items
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, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15562.png

Downloads & links

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Map

FileDownload / File: emd_15562.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 560 pix.
= 464.8 Å		0.83 Å/pix.
x 560 pix.
= 464.8 Å		0.83 Å/pix.
x 560 pix.
= 464.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.036932096 - 0.06032497
Average (Standard dev.)-0.000673628 (±0.0010782134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 464.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15562_msk_1.map
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Half map: #1

Fileemd_15562_half_map_1.map
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Half map: #2

Fileemd_15562_half_map_2.map
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Sample components

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Entire : mitochondrial ATP synthase dimer from Trypanosoma brucei

EntireName: mitochondrial ATP synthase dimer from Trypanosoma brucei
Components
  • Organelle or cellular component: mitochondrial ATP synthase dimer from Trypanosoma brucei
    • Protein or peptide: ATP synthase gamma subunit
    • Protein or peptide: ATP synthase, epsilon chain, putative
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
    • Protein or peptide: ATPase subunit 9, putative
  • Ligand: URIDINE 5'-TRIPHOSPHATE

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Supramolecule #1: mitochondrial ATP synthase dimer from Trypanosoma brucei

SupramoleculeName: mitochondrial ATP synthase dimer from Trypanosoma brucei
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondrion

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Macromolecule #1: ATP synthase gamma subunit

MacromoleculeName: ATP synthase gamma subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 34.472254 KDa
SequenceString: MSGKLRLYKE KLEGYNRFYS IVKTIKMVTL AKYRAAQGRI RTRDFSLRYT ELAFSKPQAS RDAVVAAKNA LVYIPITTNR GSCGALNSN IVRCIDSVVS SKMVLMPVGK RGIDSFSKLY PDEFRYGIIN DMKESMHFGY ATFVIENAYE VSKDADRYQV I FNRFVSAG ...String:
MSGKLRLYKE KLEGYNRFYS IVKTIKMVTL AKYRAAQGRI RTRDFSLRYT ELAFSKPQAS RDAVVAAKNA LVYIPITTNR GSCGALNSN IVRCIDSVVS SKMVLMPVGK RGIDSFSKLY PDEFRYGIIN DMKESMHFGY ATFVIENAYE VSKDADRYQV I FNRFVSAG VQRNAVYNIP SYEKWKEDLA DAASSDNQKN RYLFANALQN EEEQLIRDFF DFHAALAVLN AVGENELSEQ AA RLVAVEG QLTNISSLQQ RTSSLYNKTR QFGITAALIE ILSAMSSLEG NAMKGVRRNK FWEGAVTK

UniProtKB: ATP synthase subunit gamma, mitochondrial

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Macromolecule #2: ATP synthase, epsilon chain, putative

MacromoleculeName: ATP synthase, epsilon chain, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 20.172938 KDa
SequenceString:
MFRTFGRRLV SCTLPLLQSA PHDLPEGFEF MEHKVVNKDI HAPHENLETL RLTLTRQDEF LLREEPVKCV TVTGTNGEYG IYPGHAYKI VQLNPSPLTV EYTDGTTKKY FVSGGFAHIN NEGSCDVNTV ECTLLDDLDL AIAEKELAAQ QAALGSAKDD K AKSVVEIR ISVIEAVIAA LKHH

UniProtKB: ATP synthase, epsilon chain, putative

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Macromolecule #3: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 8.70689 KDa
SequenceString:
MIRRSCALLS SSWRDHGISY LKYLNVCTET LHSTVKESRR AKYERWSKPC YTAQRPDGAG GQETIDKVPI HTKDY

UniProtKB: ATP synthase subunit epsilon, mitochondrial

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Macromolecule #4: ATPase subunit 9, putative

MacromoleculeName: ATPase subunit 9, putative / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 12.39887 KDa
SequenceString:
MMRRLALQSS IRRATPFATP LVASTKALNP MCSAITIREA STVAISVQGL HYVGTGLAAI ALAGVGLGIG TIFGNLLVAC ARQPNLTKM LFNYAILGFA LTEAIGLFAL MLAFLMLFS

UniProtKB: ATPase subunit 9, putative

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Macromolecule #5: URIDINE 5'-TRIPHOSPHATE

MacromoleculeName: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: UTP
Molecular weightTheoretical: 484.141 Da
Chemical component information

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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