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- EMDB-10468: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -

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Basic information

Entry
Database: EMDB / ID: EMD-10468
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane region
Map data
Sample
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
    • Protein or peptide: x 19 types
  • Ligand: x 4 types
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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: 0.025
  • 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-6tdv
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10468.png

Downloads & links

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Map

FileDownload / File: emd_10468.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.060570776 - 0.13339347
Average (Standard dev.)0.00020352937 (±0.0033610577)
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-0.0610.1330.000

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Supplemental data

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Half map: #1

Fileemd_10468_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10468_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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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: ATPTB1
    • Protein or peptide: ATPTB3
    • Protein or peptide: ATPTB6
    • Protein or peptide: ATPTB12
    • Protein or peptide: subunit a
    • Protein or peptide: subunit b
    • Protein or peptide: subunit d
    • Protein or peptide: subunit f
    • Protein or peptide: subunit i/j
    • Protein or peptide: subunit k
    • Protein or peptide: subunit 8
    • Protein or peptide: ATPEG1
    • Protein or peptide: ATPEG2
    • Protein or peptide: ATPEG3
    • Protein or peptide: ATPEG4
    • Protein or peptide: ATPEG5
    • Protein or peptide: ATPEG6
    • Protein or peptide: ATPEG7
    • Protein or peptide: ATPEG8
  • Ligand: CARDIOLIPIN
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: FRAGMENT OF TRITON X-100

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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: #1-#19
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 56.026699 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 IPADTPLLGE NAKGDQYTQP PESASIPLEQ LEWTGDTVFI PAEYRTEMED 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: ATPTB3

MacromoleculeName: ATPTB3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: ATPTB6

MacromoleculeName: ATPTB6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 21.737113 KDa
SequenceString:
MTHAELHLFD LDEFMQTYKR LQTRQDWLIE NKCKKSRLFS YVAAVIAFTV GKSATMSDEA ILAKIDPYVT SEVRVQRGAW WRSGYFTKE EVEMMTPKGP IARYYKFLLG VRRFPLKHGA LSWACGFVPA WLTFTSLNHW AQNRRLNRYL TQESVFGEMA R ELVRGKTA DEATTSVMAR VEKEILGVH

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Macromolecule #4: ATPTB12

MacromoleculeName: ATPTB12 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 11.432078 KDa
SequenceString:
MSSYTGAALA PKSERLRLAF EEKQKDHQKC IEEAKGKGLK KDELIDACAW THRKTILALK DWFAYRPPFQ DRRSKWAEYC SIRHDSGSW LGWSQKFF

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Macromolecule #5: subunit a

MacromoleculeName: subunit a / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 32.666373 KDa
SequenceString: MLNSNIYIII YGGIIMYSIM IIIQMFLYNF SNKIYIEVEI NKYILSKNNI DIYWIICNCT IIIIITTLNH IINKIGIYNM IEYNICYWL IGTGLGLYIS PFIVFGYKFF VYIMDLNNYS LNIYHNNNKM NDIQQIYNGT NYNDTMIFFI KDINNIFTIY R SINFFMNW ...String:
MLNSNIYIII YGGIIMYSIM IIIQMFLYNF SNKIYIEVEI NKYILSKNNI DIYWIICNCT IIIIITTLNH IINKIGIYNM IEYNICYWL IGTGLGLYIS PFIVFGYKFF VYIMDLNNYS LNIYHNNNKM NDIQQIYNGT NYNDTMIFFI KDINNIFTIY R SINFFMNW LYQMIYYGVR MWLVFVLHSF SLGSFGELIT VITDNNLIFN VFYIGLLGLG FILYLIVIFY LGIQIYVYIS FS LSFLHST ILLFLVNYIP HYNNKSIFNT FTNKSIY

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Macromolecule #6: subunit b

MacromoleculeName: subunit b / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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 d

MacromoleculeName: subunit d / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: subunit f

MacromoleculeName: subunit f / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 11.193877 KDa
SequenceString:
MAPLYPVLSQ ASLYKRHFFK NIKLFHVVFY VGAPCVTFGT AAWSGSNRNS REAIFMVIEE RHGWDNFKKL SSHQQGVIMQ EAAQESLLA RNKGELHLP

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Macromolecule #9: subunit i/j

MacromoleculeName: subunit i/j / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 12.529404 KDa
SequenceString:
MVYTNWQSSY TRLFVSKPWM WHPLAWMTLS VGIWWKFGKE SLCNERSFYI HTHPKWAPHK FHTVYNWSRD PIKWTLAEQY ASIIRNTNT DIEAVLKIKL PANAN

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Macromolecule #10: subunit k

MacromoleculeName: subunit k / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 12.739871 KDa
SequenceString:
MAFGRTRPTL SSPLVPVWND LRALQVFTSQ EYMQKRGPGF TNTLEYKLSC LNPVKWYDMM KVMPGGKAFV GTALGLALFG GWGVEFVKN ISVMTKEKPP IDWNNEKLGH LTRS

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Macromolecule #11: subunit 8

MacromoleculeName: subunit 8 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 7.011208 KDa
SequenceString:
LIPVSLVDLI NINIIFYILL LYTLLLFFIP LFLASINYTY HYIYKYYNYN YNFINNN

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Macromolecule #12: ATPEG1

MacromoleculeName: ATPEG1 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.738803 KDa
SequenceString:
MSLAKVWMYA SWIPRGIPKA MANELSSAAA ALAHPEAIAR VAQLESQGKN PYRVARAEFW QMYLACWPYR FRNTVVEWET CKAKVLKGS VDLQDIVDLL YLLAWAYLFW ILGEIYGRGS LYGYRFDGEI HRQEAQNVIL YKEKEAQEMA VVMEKLEKEI Q EWLKTMEQ E

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Macromolecule #13: ATPEG2

MacromoleculeName: ATPEG2 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 16.210519 KDa
SequenceString:
MPLPNAVVQG YTSVRGPKRP LDHFYGRTPL NIDTLWHWVK FPHRYDNLRF AVCFWAFLVS AHFANKKQRN LRVEWEKNME IQKKLHPSG LWSEEQAFAA AEKLGRPKAG HPMRVFEDGY QQFDLKPKLF DPDEEAHH

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Macromolecule #14: ATPEG3

MacromoleculeName: ATPEG3 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 13.807529 KDa
SequenceString:
MADHNKKDVG SWASPNEHLM FFDFSSWLLV DFGKRWERWV SFKKSFLTTT RSPYWSPQFF LLTFFQLRNS NVKLCENWNW APKGDDFNL LHNSAAEPFG RDLKAHLERE AGAKHHH

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Macromolecule #15: ATPEG4

MacromoleculeName: ATPEG4 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 13.703778 KDa
SequenceString:
MGGDAHAAPA EKPDPALDAT KALPKALEEV EFFQSYAVRR KTGFHLFNRA TGSPTIVGPM FYNLYNFVRI GRVSKYVCWL SLPLVFQRM WMKNRATGME YDIDLENYAP FEAKKNPMHG H

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Macromolecule #16: ATPEG5

MacromoleculeName: ATPEG5 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 10.825277 KDa
SequenceString:
MSLPTFFLAP PLTEPFRARH RRKCIEKKDT FFQCLDKNKN ETEPCEVEAS GYSQECPDSW RRYFNEQRWK ALELKGEVKH ANLKNTQQH F

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Macromolecule #17: ATPEG6

MacromoleculeName: ATPEG6 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 9.236822 KDa
SequenceString:
MFGVTRKLLG ELSEYVEVNE KGMPKPQALS LWNMPYAKRR ALTKFARGVR WQFIVLFIAL YNFKNRDDSH LLRRGAYN

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Macromolecule #18: ATPEG7

MacromoleculeName: ATPEG7 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.861477 KDa
SequenceString:
MMRISRKLLV PVANFRPKKP WDGPWGIQIS QKKDRPFIAM WILFPLLLVD HLTREYYAYW HSSKVPVTDV FGDF

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Macromolecule #19: ATPEG8

MacromoleculeName: ATPEG8 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 7.441788 KDa
SequenceString:
MGGKASEAVT IAFRFPHRTT FLVKQNVGQK LNKGHQTFWQ LVAGGWLFFL LINRTSFKPK LAAPKV

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Macromolecule #20: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 20 / Number of copies: 25 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #21: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 21 / Number of copies: 8 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #22: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 22 / Number of copies: 12 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #23: FRAGMENT OF TRITON X-100

MacromoleculeName: FRAGMENT OF TRITON X-100 / type: ligand / ID: 23 / Number of copies: 16 / Formula: TRT
Molecular weightTheoretical: 352.508 Da
Chemical component information

ChemComp-TRT:
FRAGMENT OF TRITON X-100 / detergent*YM / Triton X-100

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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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 150242

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