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- EMDB-15560: membrane region of the Trypanosoma brucei mitochondrial ATP synth... -

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Basic information

Entry
Database: EMDB / ID: EMD-15560
Titlemembrane region of the Trypanosoma brucei mitochondrial ATP synthase dimer
Map data
Sample
  • Complex: mitochondrial ATP synthase dimer from Trypanosoma brucei
    • Protein or peptide: x 15 types
  • Ligand: x 6 types
Function / homology
Function and homology information


kinetoplast / ATP biosynthetic process / nuclear lumen / ciliary plasm / : / proton-transporting ATP synthase complex, coupling factor F(o) / 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) / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion / membrane / cytoplasm
Similarity search - Function
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 ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_15560.png

Downloads & links

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Map

FileDownload / File: emd_15560.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10553464 - 0.20181364
Average (Standard dev.)0.00074083573 (±0.0033686697)
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_15560_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15560_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15560_half_map_2.map
Projections & Slices
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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
  • Complex: mitochondrial ATP synthase dimer from Trypanosoma brucei
    • 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: subunit-i/j
    • Protein or peptide: ATPTB6
    • Protein or peptide: subunit-k
    • Protein or peptide: subunit-e
    • Protein or peptide: subunit-g
    • Protein or peptide: ATPTB11
    • Protein or peptide: ATPTB12
    • Protein or peptide: subunit-b
    • Protein or peptide: ATPEG3
    • Protein or peptide: ATPEG4
  • Ligand: CARDIOLIPIN
  • 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: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: mitochondrial ATP synthase dimer from Trypanosoma brucei

SupramoleculeName: mitochondrial ATP synthase dimer from Trypanosoma brucei
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 / Organelle: Mitochondrion

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Macromolecule #1: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: subunit-8

MacromoleculeName: subunit-8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: subunit-d

MacromoleculeName: subunit-d / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: ATPTB1

MacromoleculeName: ATPTB1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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 #5: subunit-f

MacromoleculeName: subunit-f / type: protein_or_peptide / ID: 5 / Number of copies: 2 / 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 #6: subunit-i/j

MacromoleculeName: subunit-i/j / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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 #7: ATPTB6

MacromoleculeName: ATPTB6 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: subunit-k

MacromoleculeName: subunit-k / type: protein_or_peptide / ID: 8 / Number of copies: 2 / 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 #9: subunit-e

MacromoleculeName: subunit-e / type: protein_or_peptide / ID: 9 / 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 #10: subunit-g

MacromoleculeName: subunit-g / type: protein_or_peptide / ID: 10 / 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 #11: ATPTB11

MacromoleculeName: ATPTB11 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / 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 #12: ATPTB12

MacromoleculeName: ATPTB12 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / 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 #13: subunit-b

MacromoleculeName: subunit-b / type: protein_or_peptide / ID: 13 / Number of copies: 2 / 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 #14: ATPEG3

MacromoleculeName: ATPEG3 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / 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 #15: ATPEG4

MacromoleculeName: ATPEG4 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427
Molecular weightTheoretical: 7.649776 KDa
SequenceString:
MLLGGFVPRR FSQFNRDPCW MFFIFSVGFW LGEYPAMMIK YNARDLVYDP HRYVWSHHDD HH

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Macromolecule #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 24 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 17 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #18: 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: 18 / Number of copies: 4 / 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 #19: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 19 / Number of copies: 4 / 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 #20: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 20 / Number of copies: 8 / 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 #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100605
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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