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- EMDB-10470: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -

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Basic information

Entry
Database: EMDB / ID: EMD-10470
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, rotor, rotational state 1
Map data
Sample
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
    • Protein or peptide: ATP synthase F1 subunit gamma
    • Protein or peptide: F-type H+-transporting ATPase subunit delta
    • Protein or peptide: ATP synthase F1 subunit epsilon
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATPEG1
Keywordsmitochondria / ATP synthase / MEMBRANE PROTEIN
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMuhleip A / Amunts A
CitationJournal: Elife / Year: 2019
Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts /
Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids.
History
DepositionNov 10, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseNov 27, 2019-
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: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tdx
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10470.png

Downloads & links

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Map

FileDownload / File: emd_10470.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.086183734 - 0.15326795
Average (Standard dev.)0.00025058468 (±0.0021981446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 461.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z462.000462.000462.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-420-29
NX/NY/NZ887886
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0860.1530.000

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Supplemental data

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Mask #1

Fileemd_10470_msk_1.map
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Half map: #2

Fileemd_10470_half_map_1.map
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Half map: #1

Fileemd_10470_half_map_2.map
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Sample components

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Entire : Euglena gracilis mitochondrial ATP synthase dimer

EntireName: Euglena gracilis mitochondrial ATP synthase dimer
Components
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
    • Protein or peptide: ATP synthase F1 subunit gamma
    • Protein or peptide: F-type H+-transporting ATPase subunit delta
    • Protein or peptide: ATP synthase F1 subunit epsilon
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATPEG1

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Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer

SupramoleculeName: Euglena gracilis mitochondrial ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: ATP synthase F1 subunit gamma

MacromoleculeName: ATP synthase F1 subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 35.110375 KDa
SequenceString: MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA ...String:
MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA SQKLAIFNLP KFEDWKQKLE EDSAGDGKIE EDGLLQSLPM KTALGELEET AVEDFYNFHS CLAVLNAVSE NE LSEYAAR IVAVENQLGN ITGLMQLADY TYNKTRKELI TAELLEIIGT MTAMHAGKKV GLKKTEFWK

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Macromolecule #2: F-type H+-transporting ATPase subunit delta

MacromoleculeName: F-type H+-transporting ATPase subunit delta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.559953 KDa
SequenceString:
MRASRTLLLS VSRFMRQDPR KFFPDNGFRF FDGPEDSFGD GNIPAQIILT LTRQDEFILK QEPVAAITIR TNEGEMGVLA GHEYTVQQL APGILEVEYE GGKKDQYVIS GGFAHVNDTG VVDINTVEAV PLEEIDHEKL AKALEEARAK SQSPDEAVRI Q GEIALEIF EPLEAALH

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Macromolecule #3: ATP synthase F1 subunit epsilon

MacromoleculeName: ATP synthase F1 subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.751981 KDa
SequenceString:
MSWRDAGISY LRYLSIVTRC IHEVQKEGPL LTKNVRFSTI GWKSLYLDHG ATKEYTAIPA ELEKIPENQV AQQHHA

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Macromolecule #4: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 10.820831 KDa
SequenceString:
MQRGSSITKV VRRAALARST RNAAIAYEVT VNGANLIGAG MAASGVGVPA IGVAMCFSSY MLAAARQPNM SAKLLPYCIL GFALSEALA LFTLLIALLE LFVFS

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Macromolecule #5: ATPEG1

MacromoleculeName: ATPEG1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.708709 KDa
SequenceString:
MSLAKVWTYA SWIPRGIPKA MANELSSAAA ALAHPEAIAR VAQLESQGKN PYRVARAEFW QMYLACWPYR FRNTVVEWET CKAKVLKGS VDLQDIVDLL YLLAWAYLFW ILGEIYGRGS LYGYRFDGEI HRQEAQNVIL YKEKEAQEMA VVMEKLEKEI Q EWLKTMEQ E

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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 / Number real images: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 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 magnification: 130000
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

Particle selectionNumber selected: 555269
Startup modelType of model: EMDB MAP
EMDB ID:

3559

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 150744
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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