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- EMDB-10523: Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase... -

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Basic information

Entry
Database: EMDB / ID: EMD-10523
TitleCryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, rotor-stator map
Map dataToxoplasma gondii ATP synthase dimer, rotor-stator full map
Sample
  • Complex: Mitochondrial ATP synthase dimer, rotor-stator
    • Protein or peptide: ATPTG11
    • Protein or peptide: subunit a
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: subunit c
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) / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / intracellular membrane-bounded organelle / lipid 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 / 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, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
Putative ATP synthase F0 subunit 9 / Uncharacterized protein / Putative ATP synthase / Transmembrane protein / ATP synthase subunit gamma, mitochondrial / 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: 3.5 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: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tmj
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tmj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10523.png

Downloads & links

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Map

FileDownload / File: emd_10523.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationToxoplasma gondii ATP synthase dimer, rotor-stator full map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.17156863 - 0.2713179
Average (Standard dev.)0.0010279755 (±0.0041033365)
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-0.1720.2710.001

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Supplemental data

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Mask #1

Fileemd_10523_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_10523_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_10523_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, rotor-stator

EntireName: Mitochondrial ATP synthase dimer, rotor-stator
Components
  • Complex: Mitochondrial ATP synthase dimer, rotor-stator
    • Protein or peptide: ATPTG11
    • Protein or peptide: subunit a
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: subunit c

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Supramolecule #1: Mitochondrial ATP synthase dimer, rotor-stator

SupramoleculeName: Mitochondrial ATP synthase dimer, rotor-stator / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Molecular weightTheoretical: 127 KDa

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Macromolecule #1: ATPTG11

MacromoleculeName: ATPTG11 / 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: 15.425367 KDa
SequenceString:
MVRNQRYPAS PVQEIFLPEP VPFVQFDQTA PSPNSPPAPL PSPSLSQCEE QKDRYRDISS MFHRGVAGAE QVREAYNSMA KCFRRVSVA EVLESDPAFR QARNFTMDLK QAEDDQRYKQ LQYGRVPSIL TKYHL

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Macromolecule #2: subunit a

MacromoleculeName: subunit a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote)
Strain: ATCC 50853 / GT1
Molecular weightTheoretical: 24.56257 KDa
SequenceString: MAAGSRFPFC TAARLSSRGT LPRLGEATFF AGAESQRSAG AFAKTLQRPF LRAPSTQLFP VGNRLGVSSA RALVANAMEP RRFFAAAAS AKATHALQPT GTGSVAFTRP GQGSNAQFQT SLADKTRGLL GVGFLRPTKM ASFAATFLLN FRFYFMYMAR T TFQAVRPL ...String:
MAAGSRFPFC TAARLSSRGT LPRLGEATFF AGAESQRSAG AFAKTLQRPF LRAPSTQLFP VGNRLGVSSA RALVANAMEP RRFFAAAAS AKATHALQPT GTGSVAFTRP GQGSNAQFQT SLADKTRGLL GVGFLRPTKM ASFAATFLLN FRFYFMYMAR T TFQAVRPL LAFSVFGEVM KLVLATMSSG LFSFLFSFVL AFEVFYFFLQ CYISYTFLTM FFTVLF

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Macromolecule #3: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 3 / 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 #4: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / 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: 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 #5: ATP synthase subunit epsilon

MacromoleculeName: ATP synthase subunit epsilon / 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: 8.492709 KDa
SequenceString:
MWRSSGVSFT RYASEMAALL RQCLKEPYRT QAMQRNQIHL KETVYQQGQV LTRETFNDIK KAFEAAAKHA GEK

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Macromolecule #6: subunit c

MacromoleculeName: subunit c / type: protein_or_peptide / ID: 6 / 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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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: 3.5 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-6tmj:
Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, rotor-stator model

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