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- EMDB-10469: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -

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Basic information

Entry
Database: EMDB / ID: EMD-10469
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, peripheral stalk, rotational state 1
Map dataNone
Sample
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1
    • Protein or peptide: ATPTB1
    • Protein or peptide: subunit d
    • Protein or peptide: ATPTB3
    • Protein or peptide: ATPTB4
    • Protein or peptide: oligomycin sensitivity conferrring protein (OSCP)
    • Protein or peptide: subunit b
    • Protein or peptide: subunit 8
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tdw
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10469.png

Downloads & links

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Map

FileDownload / File: emd_10469.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.06821588 - 0.11575093
Average (Standard dev.)0.0001868141 (±0.0016458264)
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-0.0680.1160.000

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Supplemental data

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Mask #1

Fileemd_10469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10469_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10469_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Euglena gracilis mitochondrial ATP synthase dimer, perpipheral st...

EntireName: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1
Components
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1
    • Protein or peptide: ATPTB1
    • Protein or peptide: subunit d
    • Protein or peptide: ATPTB3
    • Protein or peptide: ATPTB4
    • Protein or peptide: oligomycin sensitivity conferrring protein (OSCP)
    • Protein or peptide: subunit b
    • Protein or peptide: subunit 8

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Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral st...

SupramoleculeName: Euglena gracilis mitochondrial ATP synthase dimer, perpipheral stalk region in rotational state 1
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: ATPTB1

MacromoleculeName: ATPTB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 56.010633 KDa
SequenceString: MTAVVKNLAK LPAATSQILT NVSKLQTFHG LLEERRDKYA PLAYHTYDNL KQKTTWHPIA HAWVDEGLPV SKKEYNEYCW LKKDMQRLL PLASPFVFGI YGILPLAVWL SNDGYLPSAF SSKKDIVSKK LEWYSSYGDD LRQQVGPMLQ HRLKRHLRGT L NNEHRLML ...String:
MTAVVKNLAK LPAATSQILT NVSKLQTFHG LLEERRDKYA PLAYHTYDNL KQKTTWHPIA HAWVDEGLPV SKKEYNEYCW LKKDMQRLL PLASPFVFGI YGILPLAVWL SNDGYLPSAF SSKKDIVSKK LEWYSSYGDD LRQQVGPMLQ HRLKRHLRGT L NNEHRLML DEVTESYKEI FYSHYTGQLR DVRKCAHLRL YDGTSTVLLL TNKEPVELTS ELLQKWNAIK AAKLSPEEEK KA RNEALIE AYKEQELHGG PHVKHMQGYG IPSDTPLLGE NAKGDQYTQP PESASIPLEQ LEWTGDTVFI PAEYRTEVED WGR ELTKLA NQFLLLPWRF VSNAWNQRRL VSWFEEILQE DALIAKEGGV QALSDDELKV ALLDRAVIRC DEELTRGDME ARYK EISWL MSLRNPFIVL AWQTGYYRST YSPEDDLPEA SILPKLNRTV LDVDVHNELA PDHPEKPLPR VHPALYPNSH LALAK EVAV LAK

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Macromolecule #2: subunit d

MacromoleculeName: subunit d / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 53.928289 KDa
SequenceString: MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE ...String:
MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE GDVPPGAVEC LPGQVIRTKV NGEDVMLEID EVDPGYQVCW FKPDVPLPEN AEILWSYPYE PTAALPTGTT WE EGQANVL IPAEPTPEAA VWPPTPVTNV YAPMAEKLAL KSNPELKVLF KEALLQPAKL LPLDVDYQCS HDREVVEAKR DRY LTALVE AEQAPPLPFT PDVLQLQLEH NVLKGELIDR LRALEYTIVT EQLQARLHER RLRGDVIDEW EELDYHPLVR DDTY LAIDF GDPTFGRYIW KLFPHTDGDE ECMFKDTRLD VLPPQVNPLN AILAQHTAQT PVHRSLEKRL WTEVRATAVS E

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Macromolecule #3: ATPTB3

MacromoleculeName: ATPTB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 35.175836 KDa
SequenceString: MAAKTIPFVA STALGERLFA GVQKVLAAAK APVSLVQTDA KFAPADAKYL LAEPLSAAAT GELANKYGLS SKVTSGAASQ FYPNSIYPS LNVEVVQNLY ALSNPAFSSL SATTTKAVTV KDESAIKLAE LQKETERNIS SFFRDEANKS VQATLRLACD K AIKTKADK ...String:
MAAKTIPFVA STALGERLFA GVQKVLAAAK APVSLVQTDA KFAPADAKYL LAEPLSAAAT GELANKYGLS SKVTSGAASQ FYPNSIYPS LNVEVVQNLY ALSNPAFSSL SATTTKAVTV KDESAIKLAE LQKETERNIS SFFRDEANKS VQATLRLACD K AIKTKADK KTVMVVTKPH GDAFDDLLAQ VTKSESDGRA DELRNSSVSV EPTLVGNAWP KLVMFPEGVN VVVCGPNASG DQ VAQLFVG IAGGTGMVAQ QLVGDAVVFT SANAEDNENP TGALLAASNL LTALGHEAEA KKIAAAVAKA YTTDRILPKE LPG GKADLE AFIDAVAKHA SA

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Macromolecule #4: ATPTB4

MacromoleculeName: ATPTB4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 18.83351 KDa
SequenceString:
MFRGFRPVLA ADAVKFQTLY NVLTGKQHLK DQVPVKDCNL TAIFGASWKA DLNKWFDSEY APKLPAAERD SAKKSLDLYL KRVDLTRYT REELTTYGIL ACGPGKVDAL TEKHLLETGK ARLEELTAGL GNKDEGVNAF RKEVEQEGKY ANWPAEKSKA L ADKVIAAS P

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Macromolecule #5: oligomycin sensitivity conferrring protein (OSCP)

MacromoleculeName: oligomycin sensitivity conferrring protein (OSCP) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 29.56452 KDa
SequenceString: MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL ...String:
MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL HKESPLKDYK LVLETKVDPS IGGGYILEVC NQVVNRSAAA AAAETAALAK ASAAQVDWTS LPAAPPRPSP SA PDTLIRL LGSVVDDLAD ADKVEQKYGA

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Macromolecule #6: subunit b

MacromoleculeName: subunit b / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 12.673109 KDa
SequenceString:
MPSTSPADKD VPMSILHTHG LSYVNWCMSL APGLLVFEGF FRARYYRSRV PPSRTVLMNG LKMRMFSLAR QQAPKIVHKP VLSPIPEHL RLVKNVAQVQ IDMLKLLNAQ AAK

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Macromolecule #7: subunit 8

MacromoleculeName: subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 7.112312 KDa
SequenceString:
LIPVSLVDLI NINIIFYILL LYTLLLFFIP LFLASINYTY HYIYKYYNYN YNFINNNT

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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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
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: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 555269
CTF correctionSoftware - Name: RELION
Startup modelType of model: EMDB MAP
EMDB ID:

3559

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 150744

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