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- EMDB-15566: rotational state 1d of the Trypanosoma brucei mitochondrial ATP s... -

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Basic information

Entry
Database: EMDB / ID: EMD-15566
Titlerotational state 1d 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: x 25 types
  • Ligand: x 9 types
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 / ciliary plasm / nuclear lumen / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism ...H+-transporting two-sector ATPase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / kinetoplast / ATP biosynthetic process / ciliary plasm / nuclear lumen / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ADP binding / mitochondrial membrane / hydrolase activity / mitochondrial inner membrane / 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / 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
ATP synthase gamma subunit / 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 gamma subunit / 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)
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_15566.png

Downloads & links

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Map

FileDownload / File: emd_15566.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.06306089 - 0.111326315
Average (Standard dev.)-1.1171992e-05 (±0.0024004027)
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_15566_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_15566_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_15566_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: subunit-e
    • Protein or peptide: subunit-g
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: subunit-8
    • Protein or peptide: subunit-d
    • Protein or peptide: ATPTB1
    • Protein or peptide: subunit-f
    • Protein or peptide: ATPTB3
    • Protein or peptide: ATPTB4
    • Protein or peptide: subunit-i/j
    • Protein or peptide: ATPTB6
    • Protein or peptide: subunit-k
    • Protein or peptide: ATPTB11
    • Protein or peptide: ATPTB12
    • Protein or peptide: subunit-b
    • Protein or peptide: ATPEG3
    • Protein or peptide: ATPEG4
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta, mitochondrial
    • 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: ATP synthase subunit p18, mitochondrial
    • Protein or peptide: OSCP
    • Protein or peptide: ATPase subunit 9, putative
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 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
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • 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-#25
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 / Organelle: Mitochondrion

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Macromolecule #1: subunit-e

MacromoleculeName: subunit-e / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 10.448932 KDa
SequenceString:
MSAKAAPKTL HQVRNVAYFF AAWLGVQKGY IEKSANDRLW VEHQRKVRQQ NVERQQALDS IKLMQQGVRA TTPGQLEGVP AELQQLAEA FTK

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Macromolecule #2: subunit-g

MacromoleculeName: subunit-g / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972
Molecular weightTheoretical: 16.092668 KDa
SequenceString:
MSSTKCAVAC KIMTPLCNAA SKVQARSAKK LAALTDAGIQ KTISEHNANG TDAAVSSTKR YLAEQRQLFH YRVVRFFDEC HYIISGEYF AQYTKVNLIW DLRFLTKLVV LFLIGTVLGR QSIFPPIDPD SPLVEALVTK VNPNY

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Macromolecule #3: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 28.708406 KDa
SequenceString: MFLFFFCDLF WLRLLLCMYY CVWSRLCFIV YFNCLMLIFD FLLFCLFDLY LFVGLCLFLL LWFMLFNLYS LILYYCITYL NLYLLFCIV FLLYIAFLFL FCFLCDFFLF NNLLVGDSFM DVFFIRFLLC FLECFSLLCR CLSTFLRLFC NLLSSHFLLL M FFDFFYFI ...String:
MFLFFFCDLF WLRLLLCMYY CVWSRLCFIV YFNCLMLIFD FLLFCLFDLY LFVGLCLFLL LWFMLFNLYS LILYYCITYL NLYLLFCIV FLLYIAFLFL FCFLCDFFLF NNLLVGDSFM DVFFIRFLLC FLECFSLLCR CLSTFLRLFC NLLSSHFLLL M FFDFFYFI FVFFFYGVFC YWFILFIFVF CFCLLFYVFL YLLDLFAAIL QLFIFCNMIL QLIMDFLLFL LFV

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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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Macromolecule #6: ATPTB1

MacromoleculeName: ATPTB1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 46.883637 KDa
SequenceString: (AME)QGSWSVLKK NCSNFFPGLL AFAQQTQEAY GIWLRIYNRQ QKYGPTDFVE QSETFSPDYH KRFHSQDKNM WVDKEL CTE VSQKEVARLM TYKLDMWRMA HCAGALLATG GYAIPFGLFW LANDTWVPSS FNLTGEELRA WREAQDLYRY RSAPSYL TD TKWHFDFHAY ...String:
(AME)QGSWSVLKK NCSNFFPGLL AFAQQTQEAY GIWLRIYNRQ QKYGPTDFVE QSETFSPDYH KRFHSQDKNM WVDKEL CTE VSQKEVARLM TYKLDMWRMA HCAGALLATG GYAIPFGLFW LANDTWVPSS FNLTGEELRA WREAQDLYRY RSAPSYL TD TKWHFDFHAY PWNETQERAW DDLFEKNDVR RDPKVVRPAA EMYDGFIKFE LIRRKSLRHL CRSMNIPTFP MLARLCNG T RVRDYWNLAW CEDYMVITQR LHESMTDEEL YDYAWRRYLA PYDKNLNREQ LMERVEDYFE FLGPDFVAHG KAPNLVILT NYVLGYYNDP AYLEGDISEL DKNDYDHLAS WGKDAFLRRL EFENGPLRDQ VEAHTQRLLA ERAAIAKGDN AAAVEGRHTA

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Macromolecule #7: subunit-f

MacromoleculeName: subunit-f / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 17.182668 KDa
SequenceString:
MVLFSTYRSS RLVSKEFLHG PVMRFRALGE YYFQRAWNGT LNWALPGEYR LYAVMIPFIY FYHRWHNDHT LDRDHVEKAM IMRWGGTLE DVRKLSAKDQ LRVRCFTDIE KLYSAYGPKD TYLQPPGDTL PGKDFYRKAG GAQAHH

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Macromolecule #8: ATPTB3

MacromoleculeName: ATPTB3 / type: protein_or_peptide / ID: 8 / 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 #9: ATPTB4

MacromoleculeName: ATPTB4 / type: protein_or_peptide / ID: 9 / 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 #10: subunit-i/j

MacromoleculeName: subunit-i/j / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 12.661607 KDa
SequenceString:
MVYTRWKCDR LPVFQLKLFT QEYPMHAAVG IFTIIFLWKH MSHCSEETER KYGWWAGYPY WRDPIARRNE TKYKQMIINN DVDITHPKW TGCSVEQLEE LSRVV

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Macromolecule #11: ATPTB6

MacromoleculeName: ATPTB6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972
Molecular weightTheoretical: 20.307389 KDa
SequenceString:
MTKYELKMQY FDEWMIRWRK FQTESDWEIE KGRQWWRRFN MAVSGALFCG LVLYTSGTAT LKRQYGLPHF FDIGVDGQAK ETMLKTLTS RWRYTPQGYG RVLITGVPTY ILFVTLEHYR ERRRMQQYLQ QNTVFGEQMR RLLSTGKIEE YLPVNIKATL P ASQQAIYN Y

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Macromolecule #12: subunit-k

MacromoleculeName: subunit-k / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 14.531121 KDa
SequenceString:
MLRRSSAALI RRTPVRHSGG ELFVRPKLEE IPPADQCRGF FGPLNDSLKF LRLLDIKWMM NRAVAMRREY LIATPTLFTF IWMFTWKGA VIYFWGDRAP PRRMDWNTEE TGRLPLGFKP TPAPL

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Macromolecule #13: ATPTB11

MacromoleculeName: ATPTB11 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 17.929576 KDa
SequenceString:
MLRKTPLFAM ATTRKALVGN GPTFSTGGEC MNTCDIQNAF PMNDRGVRSS SPFQEPNTAI YDSYLAWTYF QPMDVHIEKL PAPEAKYYQ RHTKKPWDVS STELTEIQSR KKYFQTLGYL VAFIYLYFLM PKEKSFSGLS GPDGHWIMLP KGRPELF

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Macromolecule #14: ATPTB12

MacromoleculeName: ATPTB12 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 11.676294 KDa
SequenceString:
MSSGFHFHDV SNDAIKGMPP SEALHKHLEN AQLAHRICLA KALKAGEPPV EKCALTWGEV LIRYQAWSEY RPPFQDSVAQ AKYKKYWSK KRQEEDDKNP FK

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Macromolecule #15: subunit-b

MacromoleculeName: subunit-b / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972
Molecular weightTheoretical: 12.325279 KDa
SequenceString:
MLRRLVPRVM MAPMGGATAL CTSRGYNMLV FRDPKRRPQL SEEERAKVVV NQAEWPEEFK DFDPDDPYKN SPEIIKGMSS WNLFLWGVE CAFIYQFYEL VFPKSI

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Macromolecule #16: ATPEG3

MacromoleculeName: ATPEG3 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 12.293796 KDa
SequenceString:
MTENIEAVMS DFWSNPADHF RPNLKALTLY AERQHYVDRW LHVKERWLAP WYLPWWSPLF QLGTWYSQRS RNLFLVENHL SYRPYKFRR NDEDRNNPY

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Macromolecule #17: ATPEG4

MacromoleculeName: ATPEG4 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 7.649776 KDa
SequenceString:
MLLGGFVPRR FSQFNRDPCW MFFIFSVGFW LGEYPAMMIK YNARDLVYDP HRYVWSHHDD HH

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Macromolecule #18: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 63.574465 KDa
SequenceString: MRRFGSKFAS GLASRCALAC PLASAATAPA GASTTSSTSS AQKSFFKTTE MIGYVHSIDG TIATLIPAPG NPGVAYNTII QIQVSPTTF AAGLVFNLEK DGRIGIILMD NITEVQSGQK VMATGQLLHI PVGAGVLGKV VNPLGHEVPV GLVTRSRRLL D STLGKVDT ...String:
MRRFGSKFAS GLASRCALAC PLASAATAPA GASTTSSTSS AQKSFFKTTE MIGYVHSIDG TIATLIPAPG NPGVAYNTII QIQVSPTTF AAGLVFNLEK DGRIGIILMD NITEVQSGQK VMATGQLLHI PVGAGVLGKV VNPLGHEVPV GLVTRSRRLL D STLGKVDT GAPNIVSRSP VNYNLLTGFK AVDTMIPIGR GQRELIVGDR QTGKTSIAVS TIINQVRINQ QILSKNAVIS IY VSIGQRC SNVARIHRLL QSYGALRYTT VMAATAAEPA GLQYLAPYAG VTMGEYFMNR GRHCLCVYDD LSKQAVAYRQ ISL LLRRPP GREAYPGDVF YLHSRLLERA AMLSPGKGGG SVTALPIVET LSNDVTAYIV TNVISITDGQ IYLDTKLFTG GQRP AVNIG LSVSRVGSSA QNAAMKGVAG KLKGILAEYR KLAADSVGGQ QVQTIPMIRG ARFVALFNQK QPSYFMNAIV SLYAC LNGY LDDVKVQYVK FYEYLLVHRD LGIMYGTAKN KFFYMYVQEL NYLIRFFTLN SPILHGELEE MLKQHTHLFL QHYQSK MNA IKSEKDVKAL KNLLYSCKRA V

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Macromolecule #19: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 55.836879 KDa
SequenceString: MLTRFRSAVL RGAVSITGAR AASTAPVADH KGRVGHVSQV IGAVVDVHFA DGVPPVLTAL DVVDKLGRDE PLTLEIVQHL DAHTGRCIA MQTTDLLKLK AKVVSTGGNI SVPVGRETLG RIFNVLGDAI DQRGPVGEKL RMPIHAVAPK LADQAAEDAV L TTGIKVID ...String:
MLTRFRSAVL RGAVSITGAR AASTAPVADH KGRVGHVSQV IGAVVDVHFA DGVPPVLTAL DVVDKLGRDE PLTLEIVQHL DAHTGRCIA MQTTDLLKLK AKVVSTGGNI SVPVGRETLG RIFNVLGDAI DQRGPVGEKL RMPIHAVAPK LADQAAEDAV L TTGIKVID LILPYCKGGK IGLFGGAGVG KTVIIMELIN NVAKGHGGFS VFAGVGERTR EGTDLYLEMM QSKVIDLKGE SK CVLVYGQ MNEPPGARAR VAQSALTMAE YFRDVEGQDV LLFIDNIFRF TQANSEVSAL LGRIPAAVGY QPTLAEDLGQ LQE RITSTT KGSITSVQAV YVPADDITDP APATTFSHLD ATTVLDRAVA ESGIYPAVNP LECASRIMDP DVISVDHYNV AQDV VQMLT KYRELQDIIA VLGIDELSEE DKLIVDRARK LVKFLSQPFQ VAEVFTGMTG HYVQLDDTID SFSGLLMGTY DQVPE MAFY MVGGINSVLE KAKKMAEEAA ELEKMRRARV AQASS

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Macromolecule #20: ATP synthase gamma subunit

MacromoleculeName: ATP synthase gamma subunit / type: protein_or_peptide / ID: 20 / 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

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Macromolecule #21: ATP synthase, epsilon chain, putative

MacromoleculeName: ATP synthase, epsilon chain, putative / type: protein_or_peptide / ID: 21 / 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

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Macromolecule #22: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 22 / 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

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Macromolecule #23: ATP synthase subunit p18, mitochondrial

MacromoleculeName: ATP synthase subunit p18, mitochondrial / type: protein_or_peptide / ID: 23 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 21.268279 KDa
SequenceString:
MMRRVYSPVF CSVAAARFAA TSAAKKYDLF GYEVDTNTAP WIEKIKKCKY YDEAGEVLVN MNVSNCPPDI ATYNATLQCI YQSPSKQST PVDNESKFCA MMDLLEEMQH RNRLKPNEES WTWVMKECVK SGQFRLGYCI QQVMETECKG CPADLVKANE A NAQKAKTE GKEHPGHLSQ QAGLFDVKVE

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Macromolecule #24: OSCP

MacromoleculeName: OSCP / type: protein_or_peptide / ID: 24 / 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 #25: ATPase subunit 9, putative

MacromoleculeName: ATPase subunit 9, putative / type: protein_or_peptide / ID: 25 / 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

+
Macromolecule #26: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 26 / Number of copies: 14 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #27: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 27 / Number of copies: 3 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #28: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 28 / Number of copies: 4 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #29: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 29 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #30: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 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
type: ligand / ID: 30 / Number of copies: 2 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

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

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Macromolecule #31: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 31 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #33: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 33 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #34: URIDINE 5'-TRIPHOSPHATE

MacromoleculeName: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 34 / 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
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23019
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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