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- EMDB-10521: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

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Basic information

Entry
Database: EMDB / ID: EMD-10521
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, OSCP/F1/c-ring map
Map dataToxoplasma gondii ATP synthase dimer, OSCP/F1/c-ring full map
Sample
  • Complex: Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 / mitochondrial inner membrane / hydrolase activity ...mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / 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 / mitochondrial inner membrane / hydrolase activity / intracellular membrane-bounded organelle / lipid binding / ATP hydrolysis activity / ATP binding / 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, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / 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 / ATP synthase subunit alpha, N-terminal domain-like superfamily / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / Putative ATP synthase F0 subunit 9 / ATP synthase F1, delta subunit protein / Putative ATP synthase / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit beta / ATP synthase subunit alpha / Putative atp synthase F1, epsilon subunit
Similarity search - Component
Biological speciesToxoplasma gondii GT1 (eukaryote) / Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMuhleip A / Kock Flygaard R / Amunts A
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Research CouncilERC-2018-StG-805230 Sweden
European Molecular Biology OrganizationALTF 260-2017 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Jana Ovciarikova / Alice Lacombe / Paula Fernandes / Lilach Sheiner / Alexey Amunts /
Abstract: Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has ...Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.
History
DepositionDec 4, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseDec 16, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by cylindrical radius
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  • Surface view with fitted model
  • Atomic models: PDB-6tmh
  • Surface level: 0.04
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tmh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10521.png

Downloads & links

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Map

FileDownload / File: emd_10521.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationToxoplasma gondii ATP synthase dimer, OSCP/F1/c-ring full map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.16569056 - 0.3292639
Average (Standard dev.)0.0010336301 (±0.004911822)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z464.800464.800464.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.1660.3290.001

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Supplemental data

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Mask #1

Fileemd_10521_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 2

Fileemd_10521_half_map_1.map
AnnotationHalfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 1

Fileemd_10521_half_map_2.map
AnnotationHalfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model

EntireName: Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model
Components
  • Complex: Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model
    • Protein or peptide: Inhibitor of F1
    • Protein or peptide: ATP synthase subunit alpha,subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: Oligomycin sensitivity conferring protein (OSCP)
    • Protein or peptide: subunit c
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model

SupramoleculeName: Mitochondrial ATP synthase dimer, OSCP/F1/c-ring model
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Molecular weightTheoretical: 460 KDa

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Macromolecule #1: Inhibitor of F1

MacromoleculeName: Inhibitor of F1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 16.167462 KDa
SequenceString:
MSSPCCVAIR RVARTTLESG RRQVDSKSTD VSPFFTGTQQ MSLPSAGMVT KIRNFSSVKF MDQKRSGEET VYFKKEDEAL LRNLLANHP EYDPKYSVDH MNAEVGSIAR DITLACQKHG MKDPSAAFMK DLISIFGAHG YAKNSK

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Macromolecule #2: ATP synthase subunit alpha,subunit alpha

MacromoleculeName: ATP synthase subunit alpha,subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Molecular weightTheoretical: 61.189168 KDa
SequenceString: MTIHSCLARR AVSVAASGAR AFASGLGARA VAVGALQSAR LLHTSSLRAA GAKISPSEMS RLLEERIAGW KTQTSTEEVG RVVSVGDGI ARLFGLEGVQ AGELVEFQNG MTGMALNLET DNVGVVIFGD DRSVLEGDSV KRTGRIVDVP IGPGLLGRVV D ALGNPIDG ...String:
MTIHSCLARR AVSVAASGAR AFASGLGARA VAVGALQSAR LLHTSSLRAA GAKISPSEMS RLLEERIAGW KTQTSTEEVG RVVSVGDGI ARLFGLEGVQ AGELVEFQNG MTGMALNLET DNVGVVIFGD DRSVLEGDSV KRTGRIVDVP IGPGLLGRVV D ALGNPIDG KGPIPAKERR RVELKAPGII PRKSVHEPMM TGLKCVDALV PVGRGQRELI IGDRQTGKTA VAVDAIINQK EI NDSTDDE SKKLYCIYVA VGQKRSTVAQ IVKALEQRDA MKYTTVVAAT ASEAAPLQFL APYSGCAMGE WFRDSGRHCV IIY DDLSKQ ATAYRQMSLL LRRPPGREAY PGDVFYLHSR LLERAAKMGD KSGGGSLTAL PVIETQAGDV SAYIPTNVIS ITDG QIFLE TELFYKGIRP AINVGLSVSR VGSAAQVKAM KQVAGTMKLE LAQYREVAAF AQFGSDLDAS TRQLLTRGTA LTELL KQRQ YSPMKNSVQV CVLYCGVKGY LDPLDPKEIS RFESLFIDYI NANHQDILKT IETEKELSEK TEAKLRAAVD EFVAMN EFK KK

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Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 59.983316 KDa
SequenceString: MASPALQTCW RNLARLSGAQ VRPSHFGAFS LGSRMSPFSS LLGARASPIA TGRAGLRFLS SAAPNPGKKP ASAAPPAGTN HGRITQVIG AVVDVHFDEQ LPPILNSLEV QGHTNRLVLE VAQHLGENTV RTIAMDATEG LVRGQKVVDT GAPIQVPVGV E TLGRIMNV ...String:
MASPALQTCW RNLARLSGAQ VRPSHFGAFS LGSRMSPFSS LLGARASPIA TGRAGLRFLS SAAPNPGKKP ASAAPPAGTN HGRITQVIG AVVDVHFDEQ LPPILNSLEV QGHTNRLVLE VAQHLGENTV RTIAMDATEG LVRGQKVVDT GAPIQVPVGV E TLGRIMNV IGEPVDECGP VPAKKTYSIH RAAPLFADQS TEPGLLQTGI KVVDLLAPYA KGGKIGLFGG AGVGKTVLIM EL INNVANK HGGFSVFAGV GERTREGNDL YHEMMTTGVI KRKKLEDGKF DFTGSKAALV YGQMNEPPGA RARVALTALS VAE YFRDEQ GQDVLLFIDN IYRFTQAGSE VSALLGRIPS AVGYQPTLAT DLGQLQERIT TTKKGSITSV QAVYVPADDL TDPA PATTF AHLDATTVLS RQIAELGIYP AVDPLDSTSR MLAPEIVGQE HYDTARATQK LLQDYKSLQD IIAILGMDEL SEEDK LVVS RARKIQRFLS QPFTVAEVFT GKPGRFVELP ETIKSAQTIL RGECDDLPEM AFYMCGGLEE VRSKAVKMAQ EAASGK

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Macromolecule #4: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 34.573031 KDa
SequenceString: MAGLASLSSV GALRGMRLVP AAHLLPLHSA FGQQTRNFGA GDLKIVAARM KSVKSIQKIT KAMKMVAASK LRMDQRRLEN GLPFATPVQ KLVQRIPVDP KEKGTLAVLA LSSDKGLCGG VNSFVAKQAR IVIKENEMAG NAVQVYGVGD KIRSALQRTF G DRFKRIMT ...String:
MAGLASLSSV GALRGMRLVP AAHLLPLHSA FGQQTRNFGA GDLKIVAARM KSVKSIQKIT KAMKMVAASK LRMDQRRLEN GLPFATPVQ KLVQRIPVDP KEKGTLAVLA LSSDKGLCGG VNSFVAKQAR IVIKENEMAG NAVQVYGVGD KIRSALQRTF G DRFKRIMT EVTRFPWNFG QACIIADRLM QDNPARLMVI YNHFKSAVAY DTLTLNVLTP TQAAQSAKEQ LNTFEFEPEK TD VWKDLQD FYYACTVFGC MLDNIASEQS ARMSAMDNAS TNAGEMISSL TLRYNRARQA KITTELVEII SGANALE

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Macromolecule #5: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 19.476082 KDa
SequenceString:
MFARAFSRFA SLAAPAPQRG WNAFVLPSRH FATAAGGANP FKNQLLLTLS SPSEAIYVRT PVRSVTVPGS EGAMTMTNGH SQTVARLKA GEIIVRKGET GDEVERFFLS DGFVLFKSPE DDSGCCTAEV LGVEVVPVSM LDKESAATAL QELLQQGAGA T DEWTKART LLGQELLSSV IRAAP

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Macromolecule #6: ATP synthase subunit epsilon

MacromoleculeName: ATP synthase subunit epsilon / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 8.492709 KDa
SequenceString:
MWRSSGVSFT RYASEMAALL RQCLKEPYRT QAMQRNQIHL KETVYQQGQV LTRETFNDIK KAFEAAAKHA GEK

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Macromolecule #7: Oligomycin sensitivity conferring protein (OSCP)

MacromoleculeName: Oligomycin sensitivity conferring protein (OSCP) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 27.669994 KDa
SequenceString: MALPLLASRR LFSSFVFRGQ PSTLSSNLSL VRIRGLHGGS LSPPSATLPR AVQLFSSRIA FSTAAAEDSG ASQTLEGRYA SALFRVAKK KNQLEKVYGD LESVRNALKD SSEFRLFVDS PAVSVQQKLD VLRQLVNRYK FDPLTGNLLT TLVENKRLPM L ARVADAFD ...String:
MALPLLASRR LFSSFVFRGQ PSTLSSNLSL VRIRGLHGGS LSPPSATLPR AVQLFSSRIA FSTAAAEDSG ASQTLEGRYA SALFRVAKK KNQLEKVYGD LESVRNALKD SSEFRLFVDS PAVSVQQKLD VLRQLVNRYK FDPLTGNLLT TLVENKRLPM L ARVADAFD AMYRKEKGEV KCLVTSAKPL SAQQQKEIVA ALQNRAGTQA RLIIDYAVSP QIMGGLVVRL GEQVLDFSVA TR LDRLQSQ LLAPL

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Macromolecule #8: subunit c

MacromoleculeName: subunit c / type: protein_or_peptide / ID: 8 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 17.753504 KDa
SequenceString:
MFFSRLSLSA LKAAPAREAL PGLLSRQSFS SAGFSQFSSQ KFFFSPSRNF SQSPLFQKHT PVHCNQRIAS ALVPTQQPAM TRQNPYAMQ VGARYDAGVA SLSAAIALMS VGGVAQGIGS LFAALVSGTA RNPSIKEDLF TYTLIGMGFL EFLGIICVLM S AVLLYS

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 4860 / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 203010
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6tmh:
Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, OSCP/F1/c-ring model

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