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- EMDB-10522: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

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Basic information

Entry
Database: EMDB / ID: EMD-10522
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, peripheral stalk map
Map dataToxoplasma gondii ATP synthase dimer, peripheral stalk full map
Sample
  • Complex: Mitochondrial ATP synthase dimer, peripheral stalk
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: Oligomycin sensitivity conferring protein (OSCP)
    • Protein or peptide: subunit d
    • Protein or peptide: ATPTG12
    • Protein or peptide: subunit b
Keywordsmitochondrial / ATP synthase / peripheral stalk / OSCP / MEMBRANE PROTEIN
Function / homology
Function and homology information


photosynthetic electron transport in photosystem I / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) ...photosynthetic electron transport in photosystem I / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / 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 / ATP synthase subunit alpha, N-terminal domain-like superfamily ...ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / ATP synthase F1, delta subunit protein / ATP synthase subunit alpha / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii GT1 (eukaryote) / Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMuhleip A / Kock Flygaard R / Amunts A
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research CouncilERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 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-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tmi
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tmi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10522.png

Downloads & links

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Map

FileDownload / File: emd_10522.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationToxoplasma gondii ATP synthase dimer, peripheral stalk full map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.149573 - 0.26611784
Average (Standard dev.)0.0010349179 (±0.0037619548)
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-0.1500.2660.001

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Supplemental data

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Mask #1

Fileemd_10522_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 1

Fileemd_10522_half_map_1.map
AnnotationHalfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 2

Fileemd_10522_half_map_2.map
AnnotationHalfmap 2
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, peripheral stalk

EntireName: Mitochondrial ATP synthase dimer, peripheral stalk
Components
  • Complex: Mitochondrial ATP synthase dimer, peripheral stalk
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: Oligomycin sensitivity conferring protein (OSCP)
    • Protein or peptide: subunit d
    • Protein or peptide: ATPTG12
    • Protein or peptide: subunit b

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Supramolecule #1: Mitochondrial ATP synthase dimer, peripheral stalk

SupramoleculeName: Mitochondrial ATP synthase dimer, peripheral stalk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Molecular weightTheoretical: 68 KDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / 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

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: Oligomycin sensitivity conferring protein (OSCP)

MacromoleculeName: Oligomycin sensitivity conferring protein (OSCP) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
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

UniProtKB: ATP synthase F1, delta subunit protein

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Macromolecule #3: subunit d

MacromoleculeName: subunit d / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Molecular weightTheoretical: 61.36225 KDa
SequenceString: MQALRRGAAI PSRLLPRRDS WMSLAPFVAP NNAAAWRKLR DGAQEVQTVI ERQSTPGKPQ QIDWAKWESQ IAHKDILNCL KTFYTNQVQ ILDRALGALE TAKTPAPCEG AEKGWALFDA ALSACAKSVE KSEELLSNGA RALWVSCSNP PVWKVNTNEW L DSDQYWQA ...String:
MQALRRGAAI PSRLLPRRDS WMSLAPFVAP NNAAAWRKLR DGAQEVQTVI ERQSTPGKPQ QIDWAKWESQ IAHKDILNCL KTFYTNQVQ ILDRALGALE TAKTPAPCEG AEKGWALFDA ALSACAKSVE KSEELLSNGA RALWVSCSNP PVWKVNTNEW L DSDQYWQA FVEKHHFYSQ YQPGVVDPEA PQEVEAFKQA WHSRMGKFND RSDTPMLYAY MNELPSWEYY DLHRSAFLEH MT YFLVRTG GDFRFFPEMP PWQWLAHMEN LRFKLLSVAQ SRRSQLQLAN LERERALDFL PVDVEHHGEE YTQKFLQYET ELF QACAAR LMGHFMFLCD PFIPVQSAEA LSAVTRVDNG KGKLFSLGDD VNALFYLPEQ QRRDVERPTQ AVQTLLGHLE ATGR PFNPC YSELLHVHAE VLEERGEHWL TAPGECVSQA FLRRLRTDDP AYEVYCSYFK EMYERFAGAK EVSMEDGRKR LATIE KNAQ EEAAAYGLAL KTMGSAELAH KAREGAAKLE QLRKAQEKAA GKSAQTVQEN KM

UniProtKB: Uncharacterized protein

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Macromolecule #4: ATPTG12

MacromoleculeName: ATPTG12 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Molecular weightTheoretical: 15.400639 KDa
SequenceString:
MLNFIPKRCP SVSLLFGKRP VQRIEVGQAR HQLEIPVETI EKIYEGVDSR LEYHNKDYNA MKWKDFMKLK LDAYHLLEAS QSETAAKSA LSDLNWFSDL ADIYSGQQTM AEMDVALKAQ GEQKLSYPIQ GKNIK

UniProtKB: Uncharacterized protein

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Macromolecule #5: subunit b

MacromoleculeName: subunit b / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Molecular weightTheoretical: 64.811602 KDa
SequenceString: MNFSSSARWL AVRQSQTLGH TTRATVAAGR RVLAHSPAAT EFTSFQSLHI GGDVCKLPLA VALGAAPSAL GYGSAKHNQQ RQYATLGSG WSFSKVQYTK YRITKPWTTD TTFDDIILSQ PSKEDFAKFT KEAPLFLRFL KLVTDVEGRQ EAFIQFAKRC E NGLTVEKD ...String:
MNFSSSARWL AVRQSQTLGH TTRATVAAGR RVLAHSPAAT EFTSFQSLHI GGDVCKLPLA VALGAAPSAL GYGSAKHNQQ RQYATLGSG WSFSKVQYTK YRITKPWTTD TTFDDIILSQ PSKEDFAKFT KEAPLFLRFL KLVTDVEGRQ EAFIQFAKRC E NGLTVEKD VYVTKKELVD CLWKNGYTDT EINAFEIAFP ADYKFHYPEL AVLFDLTEED CYKYCIRQRA ATPEELVELK YT KPKNLVS SYGLCFLGVW FGLSNTVLSN AWFYSKTFPF GAVFYMLGSY FYRDIREKLW KEEKSLIHTA QENKNMGEES VYK QMKKYA TDTKCLDYLS TFRTEVEDQI ANYKVALVSQ MRRQLTERLV EKLNGIQQAE KLIQGSLQDV MIREIVSSFK DLYK SRPEL HDAAMQSAIQ GLSGSDGAMD PVGAHFKASL QELAKVNLST ATADPMGTVV QRVAAVFQKR EKEFLDTFTV KATEA QEIK TIVDKCHKGN TFDFHALSDE ELRRLEQLYS TVNNRVGFET IHENSIKPVA PLSENSKGFV EFVNTQLEIT KAKLRN ARL TAFAHAFV

UniProtKB: Uncharacterized protein

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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

Startup modelType of model: OTHER
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: 3.5 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-6tmi:
Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, peripheral stalk model

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