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- EMDB-15561: Peripheral stalk of Trypanosoma brucei mitochondrial ATP synthase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15561
TitlePeripheral stalk of Trypanosoma brucei mitochondrial ATP synthase
Map data
Sample
  • Organelle or cellular component: mitochondrial ATP synthase dimer from Trypanosoma brucei
    • Protein or peptide: OSCPOffensive Security Certified Professional
    • Protein or peptide: ATPTB4
    • Protein or peptide: ATPTB3
    • Protein or peptide: subunit-8
    • Protein or peptide: subunit-d
Function / homology
Function and homology information


kinetoplast / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial membrane / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / ATP synthase delta chain, mitochondrial / Uncharacterized protein / Uncharacterized protein
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-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15561.png

Downloads & links

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Map

FileDownload / File: emd_15561.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.06698588 - 0.114934325
Average (Standard dev.)-0.0007027486 (±0.0014592649)
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_15561_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15561_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15561_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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: OSCPOffensive Security Certified Professional
    • Protein or peptide: ATPTB4
    • Protein or peptide: ATPTB3
    • Protein or peptide: subunit-8
    • Protein or peptide: subunit-d

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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: all
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427

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Macromolecule #1: OSCP

MacromoleculeName: OSCP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 28.869924 KDa
SequenceString: MFRRLSSSAR AVVAARFYTP PEGLKKLYAS DFENSKYPLN IVPSDSVLFA KFLYKAAEEK GNFDNILSDF QKIAAAASKL PIFWERTAV VEKIPEFKQL SEPTFFTLVW MQNNGMLELI QEVAEVYETF VNAKQKKAVA KIFVAPGGEK NVEEARRVAE E LHKGLKEL ...String:
MFRRLSSSAR AVVAARFYTP PEGLKKLYAS DFENSKYPLN IVPSDSVLFA KFLYKAAEEK GNFDNILSDF QKIAAAASKL PIFWERTAV VEKIPEFKQL SEPTFFTLVW MQNNGMLELI QEVAEVYETF VNAKQKKAVA KIFVAPGGEK NVEEARRVAE E LHKGLKEL ADYTLVLKTV VDRTIVKGFA VELAGQYVNK AEGQQKQAGR ADEVDYTNLP APKPQKTVWD DNIETEVLRK YL DGLSQYD MEEAKYGV

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Macromolecule #2: ATPTB4

MacromoleculeName: ATPTB4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 17.218723 KDa
SequenceString:
MRRTFISFSA ASAAAAAPVT STKMQTLHKL LTGEVSFKNK APVKDCNIVH QFGENWATEL SAYAKTLPAE QQKIIVRQIA RVKLTRYTV AELAAYCGDG PALLDETARA ANIEQGVAFV KAKGVEAFEK YVAEESTNAN WKPEEAKKFI EDVKAKAK

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Macromolecule #3: ATPTB3

MacromoleculeName: ATPTB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 27.646643 KDa
SequenceString: MSKQLTFISA GATAAVLQSA SAIVSKVAGG RVQTKTAKEA GRHAVVVGPE TPIGVHTAVT EVPKSAQDPL FSGVSTVVVR AVLPRAAPD SVQLRDALDV YASAGIDTKE EVRSATEAFK KSAEVAVGKA KAKGVKRIVL VVKQASKHNC INELFKKIST E TIESAGLT ...String:
MSKQLTFISA GATAAVLQSA SAIVSKVAGG RVQTKTAKEA GRHAVVVGPE TPIGVHTAVT EVPKSAQDPL FSGVSTVVVR AVLPRAAPD SVQLRDALDV YASAGIDTKE EVRSATEAFK KSAEVAVGKA KAKGVKRIVL VVKQASKHNC INELFKKIST E TIESAGLT TEVVGTAAVA NQLIVNPESL GVVLLNDVAA TEQIELAFAG VVGGVSRVYH TVEGGKISAG HSFKSVALAV AQ ELRELGL SSEADKVEAA ASKNPRAVVS AL

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Macromolecule #4: subunit-8

MacromoleculeName: subunit-8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 13.750958 KDa
SequenceString:
MLRRLGANVS NMARPMNKYA VTVSPRRHLE PMSTWYLASW AMVWYYAFFF WMPMVWTDIM VPSFVYNKLP VIHFLQEKRA EQKLRRVLD ETYTEWTEEL DQAHVTDAIT RSLNI

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Macromolecule #5: subunit-d

MacromoleculeName: subunit-d / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 43.379324 KDa
SequenceString: MRRVSSPNIT IQSVRWISGV SPLLYFPPTT TSTTNREDQI NKNTNIAIQM IKRYKGEVPP HYTRKSSATI EQVEKEIDAL LGGAEKLRK TSTDDQPMDK LTLMERCLRH ALWSYHKEEG RYDFDQIGRW VVYTPEDEVK LAQLKREVEA KEKLAALRKR R EEEGLPGG ...String:
MRRVSSPNIT IQSVRWISGV SPLLYFPPTT TSTTNREDQI NKNTNIAIQM IKRYKGEVPP HYTRKSSATI EQVEKEIDAL LGGAEKLRK TSTDDQPMDK LTLMERCLRH ALWSYHKEEG RYDFDQIGRW VVYTPEDEVK LAQLKREVEA KEKLAALRKR R EEEGLPGG PVPRINWPQE YSSFIDREPV VAKRIRYDTL ASTTLERDEK QIESTLQQYR RASQDKRLDD LVDLLERFKP VL AREAIMQ RLTIKHLEGQ LGVWRYMDWC PEVRDRAELE VDITGWQWWS PLEERRLLPV RLRSVNEVRE IMSKTQAKKS AEA AERNPI VTQTSTGDNA RDRLLKEVLA LQARINQRDE VEPSQTEQKK KAHH

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201210
FSC plot (resolution estimation)

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