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- EMDB-10858: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-10858
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - central stalk/cring
Map dataLocal-resolution filtered full map of T. thermophila ATP synthase central stalk/c-ring
Sample
  • Complex: Mitochondrial ATP synthase, central stalk/c-ring
    • Protein or peptide: subunit c
    • Protein or peptide: subunit gamma
    • Protein or peptide: subunit delta
    • Protein or peptide: subunit epsilon
Keywordsmitochondria / ATP synthase / central stalk / c-ring / MEMBRANE PROTEIN
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 transmembrane transporter activity / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / mitochondrion
Similarity search - Function
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 / 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
Uncharacterized protein / ATP synthase subunit gamma / Uncharacterized protein / ATP synthase F0 subunit 9
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKock Flygaard R / Muhleip A
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts /
Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.
History
DepositionApr 14, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ynw
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10858.png

Downloads & links

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Map

FileDownload / File: emd_10858.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal-resolution filtered full map of T. thermophila ATP synthase central stalk/c-ring
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.030505672 - 0.06750972
Average (Standard dev.)0.00030259805 (±0.001806222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z498.000498.000498.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0310.0680.000

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Supplemental data

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Mask #1

Fileemd_10858_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_10858_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_10858_half_map_2.map
AnnotationHalf-map 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, central stalk/c-ring

EntireName: Mitochondrial ATP synthase, central stalk/c-ring
Components
  • Complex: Mitochondrial ATP synthase, central stalk/c-ring
    • Protein or peptide: subunit c
    • Protein or peptide: subunit gamma
    • Protein or peptide: subunit delta
    • Protein or peptide: subunit epsilon

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Supramolecule #1: Mitochondrial ATP synthase, central stalk/c-ring

SupramoleculeName: Mitochondrial ATP synthase, central stalk/c-ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: subunit c

MacromoleculeName: subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: ec: 3.6.1.34
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 8.083702 KDa
SequenceString:
MLLVKAVKVL VMGGCMLPIA FGALGTGVLF AGFNVALSRN PEETESLFNN TLMGFALIET FIFMSIGLGF FVLFAA

UniProtKB: ATP synthase F0 subunit 9

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Macromolecule #2: subunit gamma

MacromoleculeName: subunit gamma / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 32.915152 KDa
SequenceString: MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA ...String:
MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA HQVSTQGAGY DQVTLIYNHF KNAISYVVKH QELLPRAQFL NLFKYVTRHE AVEPELEYSK NYFFELYMAS SV YNALLNS SASEQASRMN AMENASKNAG EILSKLTLDY NKARQAKITM ELIEIISGAS IV

UniProtKB: ATP synthase subunit gamma

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Macromolecule #3: subunit delta

MacromoleculeName: subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 17.892537 KDa
SequenceString:
MFTRFVTQPT LLTQTQRALF SALTKKQKME VTLRTPYKEY LANFDGFSRI TAKTNEASLV IQNKTPASLY VLPPGPLKIR FTSEVKNVS GDFLHTGGWV IVHADNTCEI NVMDLFDRKE VRADQFEKGN IQDLDTLAGK YAAKSRKSTV RLFTKATTQ

UniProtKB: Uncharacterized protein

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Macromolecule #4: subunit epsilon

MacromoleculeName: subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 7.986336 KDa
SequenceString:
MCIEFAFKKA GIPIVRNFLH STEGVIYGLP QRVQRNLAIN YTVKQYKEGK AVSAKTIKTL QEAFPSKGDT K

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

Concentration0.75 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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 / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.9 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. 3.1) / Software - details: beta
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: beta
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: beta / Number images used: 61157
FSC plot (resolution estimation)

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