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- EMDB-35723: Cryo-EM map of Euglena gracilis supercomplex III2+IV2, composite -

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Basic information

Entry
Database: EMDB / ID: EMD-35723
TitleCryo-EM map of Euglena gracilis supercomplex III2+IV2, composite
Map data
Sample
  • Complex: Euglena gracilis supercomplex III2+IV2
    • Complex: Euglena gracilis supercomplex III2+IV2
      • Protein or peptide: x 30 types
  • Ligand: x 12 types
KeywordsElectron transport chain / supercomplex / membrane protein / Euglena gracilis / ELECTRON TRANSPORT
Function / homology
Function and homology information


cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / mitochondrial inner membrane / electron transfer activity / copper ion binding ...cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / mitochondrial inner membrane / electron transfer activity / copper ion binding / heme binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD ...Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
Cytochrome b / Cytochrome c1, heme protein / Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial / Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial / Cytochrome c oxidase subunit 1 / Putative NADH dehydrogenase subunit 6 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsWu MC / Tian HT / He ZX / Hu YQ / Zhou L
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor China
CitationJournal: Nat Commun / Year: 2024
Title: Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism.
Authors: Zhaoxiang He / Mengchen Wu / Hongtao Tian / Liangdong Wang / Yiqi Hu / Fangzhu Han / Jiancang Zhou / Yong Wang / Long Zhou /
Abstract: Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron ...Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III + IV and supercomplex III + IV. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
History
DepositionMar 24, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35723.png

Downloads & links

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Map

FileDownload / File: emd_35723.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 4.8
Minimum - Maximum-21.700908999999999 - 39.138244999999998
Average (Standard dev.)-0.023115411 (±1.0257444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 537.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35723_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35723_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Euglena gracilis supercomplex III2+IV2

EntireName: Euglena gracilis supercomplex III2+IV2
Components
  • Complex: Euglena gracilis supercomplex III2+IV2
    • Complex: Euglena gracilis supercomplex III2+IV2
      • Protein or peptide: MPP-beta
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1, heme protein
      • Protein or peptide: UQCRQ
      • Protein or peptide: UQCR10
      • Protein or peptide: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrialCoenzyme Q – cytochrome c reductase
      • Protein or peptide: COXEG1
      • Protein or peptide: COXEG3
      • Protein or peptide: COXEG5
      • Protein or peptide: COXEG8
      • Protein or peptide: COXEG10
      • Protein or peptide: COX5c
      • Protein or peptide: COX6a
      • Protein or peptide: COX6b-1
      • Protein or peptide: COX7c
      • Protein or peptide: Cytochrome c oxidase subunit 1
      • Protein or peptide: Cytochrome c oxidase subunit 2
      • Protein or peptide: Putative NADH dehydrogenase subunit 6
      • Protein or peptide: COX4
      • Protein or peptide: UQCRFS1
      • Protein or peptide: UQCRH
      • Protein or peptide: UQCRB
      • Protein or peptide: UQCR9
      • Protein or peptide: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
      • Protein or peptide: COX5b-2
      • Protein or peptide: COXEG4
      • Protein or peptide: COXEG6
      • Protein or peptide: COXEG7
      • Protein or peptide: COXEG9
      • Protein or peptide: COX7a
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: HEME C
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

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Supramolecule #1: Euglena gracilis supercomplex III2+IV2

SupramoleculeName: Euglena gracilis supercomplex III2+IV2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 1.4 MDa

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Supramolecule #2: Euglena gracilis supercomplex III2+IV2

SupramoleculeName: Euglena gracilis supercomplex III2+IV2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#30
Source (natural)Organism: Euglena gracilis (euglena)

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Macromolecule #1: MPP-beta

MacromoleculeName: MPP-beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 53.520293 KDa
SequenceString: MTTPSLSSIL RHTRPIFKET LRAARPTLQN ALPNGFRIAS ESKDGDTCTV GVWIDAGSRW ETEKNNGVAH FLEHMNFKGT GKRSRQDIE FGMEKMGAHL NAYTSREHTC YYVKCFKKDV PEAVDILADI LLNSKRTEQD LDAERQTIVQ EKEDVEARID E VLMDHLHS ...String:
MTTPSLSSIL RHTRPIFKET LRAARPTLQN ALPNGFRIAS ESKDGDTCTV GVWIDAGSRW ETEKNNGVAH FLEHMNFKGT GKRSRQDIE FGMEKMGAHL NAYTSREHTC YYVKCFKKDV PEAVDILADI LLNSKRTEQD LDAERQTIVQ EKEDVEARID E VLMDHLHS AAFEGSGLGL SILGPLENIQ KSITKGMIDD FVKTHYTGPR MALVGSGAVD HGQLCDLASK YFGALPTGQP KP SGFTRFL GGDKRETNQL NPLTHVAVAF QTPGISHPDA IKIKVLEQLL GSYSRDKGEA AYSCFARAIV MDFYDPKVGQ FFR PNKAGH NPIHSLNAFW APYSDVGLLG FYAIAEPGKS YGHEWENILH YAMRELIRVS RNISEEEFER AKNQLKLQTM LQLD GTTNI ADDIGRQVLS FGARVPLASF FEQLDAISRE DLIRVAHEYF YDKDPVVAVI GDTDNVPEYD ALRAVTYSVD LGRA

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Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 42.476266 KDa
SequenceString: MNKISLYRSY STTILLSPAY SLGFCASIFI VIQIISGYIL ASNYIASTNE SFNIIHNVIM RELDTGWLIR FNHINGCAFL FIVIYMHIY RSLYHNSITK TSVWIVGIIM YILICGIAFT GYSLVYGQMS LWAIVVICSL VTAIPFIGNK LLILIWGGNI V SSVTLQRI ...String:
MNKISLYRSY STTILLSPAY SLGFCASIFI VIQIISGYIL ASNYIASTNE SFNIIHNVIM RELDTGWLIR FNHINGCAFL FIVIYMHIY RSLYHNSITK TSVWIVGIIM YILICGIAFT GYSLVYGQMS LWAIVVICSL VTAIPFIGNK LLILIWGGNI V SSVTLQRI FCIHYLLPLL LILFIIIHLY NLHNVNSTGD NYFINNRYDR INFYPLLLIR DVFIGSNILI IYNIFVYYYS DL FGHPDNY VPANPLVTPS EIMPEFYLLP FYALIRAIPH KVLGIIIMVL FLLSLTNLYP IYFIRFYNNI NILQRSLLLL LLL DLVIAS KLCLLINHYE SFYLLLILSI LCVLSHHIYN TSFNFSNSIS NL

UniProtKB: Cytochrome b

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Macromolecule #3: Cytochrome c1, heme protein

MacromoleculeName: Cytochrome c1, heme protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 27.889436 KDa
SequenceString: GVDSHPPALP WPHFQWFQGL DWRSVRRGKE VYEQVFAPCH SLSFIKYRHF EAFMSKEEVK NMAASFEVDD DPDEKGEARK RPGKRFDTV VQPYKNEQEA RYANNGALPP DLSVITNARH GGVDYIYALL TGYGRPVPGG VQLSTTQWYN PYFHGGIIGM P PPLTDDMI ...String:
GVDSHPPALP WPHFQWFQGL DWRSVRRGKE VYEQVFAPCH SLSFIKYRHF EAFMSKEEVK NMAASFEVDD DPDEKGEARK RPGKRFDTV VQPYKNEQEA RYANNGALPP DLSVITNARH GGVDYIYALL TGYGRPVPGG VQLSTTQWYN PYFHGGIIGM P PPLTDDMI EYEDGTPASV PQMAKDVTCF LEWCSNPWWD ERKLLGYKTI ATLAVIAVSS GYYNRFLSGL WRSRRLAFRP FN YSK

UniProtKB: Cytochrome c1, heme protein

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Macromolecule #4: UQCRQ

MacromoleculeName: UQCRQ / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 10.079598 KDa
SequenceString:
MEGHSAYVAL EQRVNTRQKG IIQRHLSPYD VDIRGNGFRQ IYRLGMQKIR YFGLIGTPCL LVAGAYRGIW VFCERLEDER YWSNAL

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Macromolecule #5: UQCR10

MacromoleculeName: UQCR10 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 17.577297 KDa
SequenceString:
MALEIKREWH VVPATKKFAD VPTEWPAKEH ERFALPYGPS EGRIVSFMRA SRIRNRLLFT LNPTGYTEDT YVTKEALRRQ ALAESKNLW YLPERPVVAD QLETIVNRST FFVVKGHKNK GLIGIAGARH NPLVWLPTLA LGGVWAWRWA SAGTI

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Macromolecule #6: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial

MacromoleculeName: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 11.300364 KDa
SequenceString:
MQTHVRRVAL QALRPCLRAG LMAPKFPVRF ATTAVSGELL TKTPYTRPGY AAQWTCLVVL FLKNQLLMRL FFAFVAYVVA MKVFGARFH VDHDEDATPA E

UniProtKB: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial

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Macromolecule #7: COXEG1

MacromoleculeName: COXEG1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 27.278852 KDa
SequenceString: MLSRALCSRN VPMSLKALNR PGSAGKLPMQ LMKYASAVAP ISHEGTLVRI SQVKKLSELQ LHFNDSHLGE SELAAKVLGK LRKLEAEVL ARNQAFNEAH PLVFDPKRAF NDEIFLCCSL CCIIFLIFLF NQYEEFAHEL SFDIREQFGL GFYMLLGLHG S HVIFGTIM ...String:
MLSRALCSRN VPMSLKALNR PGSAGKLPMQ LMKYASAVAP ISHEGTLVRI SQVKKLSELQ LHFNDSHLGE SELAAKVLGK LRKLEAEVL ARNQAFNEAH PLVFDPKRAF NDEIFLCCSL CCIIFLIFLF NQYEEFAHEL SFDIREQFGL GFYMLLGLHG S HVIFGTIM LALLTLWGAQ GSVGPQSHAL RFTSLYVHLV DLVFIILVLA IYSANASPEL YGGIVPNILE ARTFVSVDAA GN PQIKEF

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Macromolecule #8: COXEG3

MacromoleculeName: COXEG3 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 16.394043 KDa
SequenceString:
MMQRIPFKKP NQIRGYFTRV HKYNHVPVPF ILNVGMSISI VTSFVYFTYT SLWVRPEYDR VVDPSKAYVN PVWVDYWLKL RDEKRIQGA LERSILEEEP EKAAEKILEW ARTSAQNKIL EDLKLLKPAL SPATIAQFEK

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Macromolecule #9: COXEG5

MacromoleculeName: COXEG5 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.464051 KDa
SequenceString:
MPSSMAWTIG WGFYAAWIMK ETWNLRSSSV GWTPITLMEA YKTKERYLRS KAMMERYNSE LEAVDDSNIT EEDAKKFELE KATPSISIW EQFRSNPYWK EVEEEISTDV RKTMLEKHPD YALLLEAVKK SGYSKLWHLP GPWMNEHYND GLHGRFLGWT P KAAHH

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Macromolecule #10: COXEG8

MacromoleculeName: COXEG8 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 24.49532 KDa
SequenceString: MLRVLTPAIA RPGLRCFFKD GFRDNASLEL VYRVVLKSPA VSQKLIEFYA KSLDQLSVES LSALKGTTVG IPLQPYLGDP HRVLLAYSL LPHTVETEAD GNPVVETKIG DEEQKIKIID SEVISFLAKE ILGKLGLETT PQAARQYLDS LVEGAEALYA K IAPVEPSP ...String:
MLRVLTPAIA RPGLRCFFKD GFRDNASLEL VYRVVLKSPA VSQKLIEFYA KSLDQLSVES LSALKGTTVG IPLQPYLGDP HRVLLAYSL LPHTVETEAD GNPVVETKIG DEEQKIKIID SEVISFLAKE ILGKLGLETT PQAARQYLDS LVEGAEALYA K IAPVEPSP LEKAIAEINE EIKSGTPWDT LKNRADPKEL HALKFAQLPH PITKKVEGKF KYF

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Macromolecule #11: COXEG10

MacromoleculeName: COXEG10 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 10.043338 KDa
SequenceString:
MNHERPWVFL NKVTGKWGAC GWQPFWKATS QSLNYIPDNF IALRTNGSWV RNLWQSSKVL DRGLNASGYP TVGTTDWVRI PLDAPLEA

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Macromolecule #12: COX5c

MacromoleculeName: COX5c / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 23.788312 KDa
SequenceString: YFFSRARMSL QLGHMRVGAL WQSNANSRGL PNLLKEVMAA EPIYPYTHPG LSAKQILWNT KFNLKLEKDL ISIAESAVQS QTVNKVVIP TMLTGDVNPK SPASVVAKDK YQLAKQMAEF QYKKSYFEKP WGYMFAYYCD EDRARLCGGI GYVGHHGGGD A EILSYTEY ...String:
YFFSRARMSL QLGHMRVGAL WQSNANSRGL PNLLKEVMAA EPIYPYTHPG LSAKQILWNT KFNLKLEKDL ISIAESAVQS QTVNKVVIP TMLTGDVNPK SPASVVAKDK YQLAKQMAEF QYKKSYFEKP WGYMFAYYCD EDRARLCGGI GYVGHHGGGD A EILSYTEY VSTVVYPTIF YMAITFVVSL FLMYYYIYGT FFSSTRNRFD

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Macromolecule #13: COX6a

MacromoleculeName: COX6a / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 13.079197 KDa
SequenceString:
MSTNKNVFFP PALHLKENSI FQYKFKNLAV RHDAARLGII LAGPTLFYWF TVYYFKGMPN GLPPVLLNPF VNRNYRGQKR DMPWGTDCA FLDTKCHEEK DTWAKRGPFF IIA

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Macromolecule #14: COX6b-1

MacromoleculeName: COX6b-1 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 32.995148 KDa
SequenceString: MEGFVDKIDD NKYLGKWETI LTDGRTHLPK HITFHDAAAI SARWNQQYVN DSGPVYYRHW LACQQTYGAG NEDCRKLRWW AQQITHPLH LAEWDDWWKD EHYDLQIGQH WNRICGEEFE EASNLLKDLK EKREGLAAKF RDLLKTKTAE DPMGKILHEV A QLEEPSKT ...String:
MEGFVDKIDD NKYLGKWETI LTDGRTHLPK HITFHDAAAI SARWNQQYVN DSGPVYYRHW LACQQTYGAG NEDCRKLRWW AQQITHPLH LAEWDDWWKD EHYDLQIGQH WNRICGEEFE EASNLLKDLK EKREGLAAKF RDLLKTKTAE DPMGKILHEV A QLEEPSKT PVADLVEAGT LSKEAVEAAA ALKIKELKAL RDDATWAEVK GSLLNGVTTT CSTLKKTSKV VAELKAQAEL ER NKTSAVK LDIPHMRVNY EKPGLYEYDT WFGKFLPRTP QFGFAESDEE

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Macromolecule #15: COX7c

MacromoleculeName: COX7c / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.897588 KDa
SequenceString:
MQKAVVGNLL RQLSLTRPRG HGSNLYNRVH GNLPQLYVEQ LYNTDEILDT VPHSSDPVHH MFPKCAAASP LGFRPYDNNK LWDAFVLWA IVYGVTTIFC VLHILKYPQI WKHLFETLTF QYTYQREIGE EYVWQYGGGG LNPAKWRFVK SPLEELGLVT E YRSDLDYP DDL

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Macromolecule #16: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 55.759504 KDa
SequenceString: MINNIMHMIN KYTLTTSHKI IGILYGYMGY IAGILGYIIS MLIRMELNTQ GLAIVRKVKE VTIYNNWITI HGLIMLFVFI MPVGIGFYG NYLIPMLIGT SELSMPRMNG ISFWMLIVGV VIFVISNVLM SKPISSGWTL YPPLSTRDAD NIGVNIDLSL L VVHVLGIS ...String:
MINNIMHMIN KYTLTTSHKI IGILYGYMGY IAGILGYIIS MLIRMELNTQ GLAIVRKVKE VTIYNNWITI HGLIMLFVFI MPVGIGFYG NYLIPMLIGT SELSMPRMNG ISFWMLIVGV VIFVISNVLM SKPISSGWTL YPPLSTRDAD NIGVNIDLSL L VVHVLGIS STIGSVNYIT TNKYNRHVGL TFMNINIYNF SIIVTSILLI GSLPILGVAI TGLLLDRNIN STIYDVIGDP VL YQHLFWF FGHPEVYVII LPVFGLTSLI LTSIIHKDIF GREGMMYCII SIGVVGYFVW AHHMFTVGLD IDSRSYFSIA TSI ISIPTS VKMFSYINTW ASGRGFRGNN SSWSFFSFLI CFCFGGFTGL LLSSGSLDIM LHDTYFVVGH FHTVLSLAAT FGLL IAHYF FLPIIFSYSI FESFSFYHTF LLLVGALLVF YPMHLAGLSG MARRVPEYAD IFIPFMTVGF HGTFLLIFST LTFIR SYFQ FLSHINHSNY L

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #17: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 22.443406 KDa
SequenceString: MRYGNREIES IILFFDQTII LYTSIINALI VGIIIIIRKW YNRKGICNQY IYHIKIEVIW TILPIIFLIV IVLHSVTVIY NLEINKGTN NKYINVIGNQ WYWIYNNIES RISSLGRIIL VDQPLFIKAN NNTHLIISSL DVIHSFALPT LGIKVDAIPG R INNISING ...String:
MRYGNREIES IILFFDQTII LYTSIINALI VGIIIIIRKW YNRKGICNQY IYHIKIEVIW TILPIIFLIV IVLHSVTVIY NLEINKGTN NKYINVIGNQ WYWIYNNIES RISSLGRIIL VDQPLFIKAN NNTHLIISSL DVIHSFALPT LGIKVDAIPG R INNISING LTQGLYVGYC SELCGSGHAF MPINLIVY

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #18: Putative NADH dehydrogenase subunit 6

MacromoleculeName: Putative NADH dehydrogenase subunit 6 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.414947 KDa
SequenceString:
MILNTNINYG GRNSRLCYLI PLMVHTIFLY LAYLIYYNIN LINIYLLLII IIFINIEWPL VIIYEYIYLT NYNIQNNLLY NIATFIFLE ILLFIGFYWL YINNIIHYPN NLPYNNNIAV NLLDHLNHNN NTDICLYIIL HNLLLLLYVT LILQLVHRYV Q L

UniProtKB: Putative NADH dehydrogenase subunit 6

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Macromolecule #19: COX4

MacromoleculeName: COX4 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.42748 KDa
SequenceString:
MGGDAHAHGG HGLHADPIFN GSKVVRSIQM MRSYHRLPVG PEPPHLKIRG APLHPWSMYT DKGGFFFGVG TQLPRNFFPK FLATTSAIM GVTYGLVWLY NAAGPRAKTQ TRKWKELESE DPRFPFQEIP EIYLPSDIDR DPNADCWRIL NQVPRKEKLL V EITDPLRN FDFKVAKIKE N

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Macromolecule #20: UQCRFS1

MacromoleculeName: UQCRFS1 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 27.825922 KDa
SequenceString: MFKQLSRMYS TSPAVANAVG GLATSQIRDL VGNPAKSGKP VVKMPPYLKP SQLRPSRGAY SDEFVRENYI KAADPEDPYN YRSRAFTYA AKIPMWAGLL AGTRVTVVYL MSQFMPSKSS LALANIEVDI GDIPEGKTVT IMWQGKPVFL RKRTDAEIED M RAVPMDAL ...String:
MFKQLSRMYS TSPAVANAVG GLATSQIRDL VGNPAKSGKP VVKMPPYLKP SQLRPSRGAY SDEFVRENYI KAADPEDPYN YRSRAFTYA AKIPMWAGLL AGTRVTVVYL MSQFMPSKSS LALANIEVDI GDIPEGKTVT IMWQGKPVFL RKRTDAEIED M RAVPMDAL KDPQTDEERL GEGRWAVFMA VCTHLGCVPV IDQGSYNAYF CPCHGSHYDH SGRIRKGPAP LNLEVPPFKL LD DSTLFIG NADAA

+
Macromolecule #21: UQCRH

MacromoleculeName: UQCRH / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.207571 KDa
SequenceString:
GKMAAEQVSV SELKLKFEEE CAHHHCHDIV KKVEVCEESI KGKEGKNCLF QHARLWECVD HCASPKVFAL LK

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Macromolecule #22: UQCRB

MacromoleculeName: UQCRB / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 27.404115 KDa
SequenceString: MNDAPILAKL GLSKVNTYYF QRRKHIFALP ITIPNFPLAA LGIFRSTDMF EERTLERYSR DEREKTLGKA ALLLKEAKEK GNYSELVRL DPTDPRHPYY FEHPWQSALK MDTVSLTPYQ QYLRWHCLTY RAMHEWDRQG LLYDDLMQPK ALATDPFLEE A ILRLPYNQ ...String:
MNDAPILAKL GLSKVNTYYF QRRKHIFALP ITIPNFPLAA LGIFRSTDMF EERTLERYSR DEREKTLGKA ALLLKEAKEK GNYSELVRL DPTDPRHPYY FEHPWQSALK MDTVSLTPYQ QYLRWHCLTY RAMHEWDRQG LLYDDLMQPK ALATDPFLEE A ILRLPYNQ RVERERRLSR AYDLALRREY LPDEDCIHPE DDVAYLHPYY HMVVDEHREQ HENPVDVYSR

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Macromolecule #23: UQCR9

MacromoleculeName: UQCR9 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 6.939355 KDa
SequenceString: MLANFSRFFY KTFLQSNATL IPLTLVFTY(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK) ...String:
MLANFSRFFY KTFLQSNATL IPLTLVFTY(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #24: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial

MacromoleculeName: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 51.13266 KDa
SequenceString: MKSVVRSKGT QALFRRFSSA LGDSINPNQV GVGDNVIRVN GRLFEVDKVQ EKGLKTSVLD NGTKVITLDN GGSVAQLTFL YKDGPVYEN IFNAGISSFM KHALTKDGLT SSEYITKTFL QKAGIIVHEP TVVNKSAIAF TVEGFRDTLA QPAVADKFWQ S LLFPRFSP ...String:
MKSVVRSKGT QALFRRFSSA LGDSINPNQV GVGDNVIRVN GRLFEVDKVQ EKGLKTSVLD NGTKVITLDN GGSVAQLTFL YKDGPVYEN IFNAGISSFM KHALTKDGLT SSEYITKTFL QKAGIIVHEP TVVNKSAIAF TVEGFRDTLA QPAVADKFWQ S LLFPRFSP ENVKEVKRLV ELESKETKRD SPFAYLQDIL HKTAFKGSPL GHTSFVPAYN LGYIDSNKLF DRWDAHYGFG NI AVIATNI EHEAVLAAIT DSAWVARAHN KVGGVAAPAS KYSGGEGYDV VHRAKEFDDQ FTDVYSTYTA YAFKAPGRSN LKE HAASLV IAQALSNAVS PVLNTSFAPK RLEVFYQAYD TVGLIGLSSV QASNAQLKAF KAALSKIGTL SEADLAVHKS AALL TAYGN VESWRATQAT LIDSFNTTGQ PLSPLEIVSA IKAVSADTVK SVVATMLGSP ATLVHHGDSP CAPTLDALQ

UniProtKB: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial

+
Macromolecule #25: COX5b-2

MacromoleculeName: COX5b-2 / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.736387 KDa
SequenceString:
MFRRGLVLAA SRSKSLLDSV HVFRPEFAQG KFRIDLDQPA KQNKLQQQIY TLTDDEREMY EDEPYIGVDH LYEAHKGSKE NPVVVEAIG VHGNDVFTGC LGGCHKDAAD AVAYYTIVPP NTLAVCIDCG IHFVARINEQ LTFWPDGTQP WEKVDFKAVE G FLYKHYKY GSPLMI

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Macromolecule #26: COXEG4

MacromoleculeName: COXEG4 / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.359492 KDa
SequenceString:
MSTVLSILGK RFQRSALTPK MNPFIRIRCQ GPIEEFQRGF IGEFHAFALP GACMLVASCL GTFHIIRCLV VNPELSLAKV IPEILQPFT NPNAQLKAAD GKDDDDSQVP KQWGMWGRHP NYGVLHVPFL DALNKEALAR GKDGVNMGAE YNLVFTKSMA D QVVDLILD DVQKRV

+
Macromolecule #27: COXEG6

MacromoleculeName: COXEG6 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.728172 KDa
SequenceString:
VFPSITKPLG LFKNLPRQHR AARDASIWLA ILTAGPFGIF IAFKYYADWY DKKLLMEYYK DSIVYGETYG KGKYV

+
Macromolecule #28: COXEG7

MacromoleculeName: COXEG7 / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 35.651516 KDa
SequenceString: MLRQVVRRSN PLRMQVRGSA WNFQELMESR IPDYKGRPNR SGAELEQVKA ALPKIEFMTS YEFDVLTKTR SNLTKEYSYQ RDMRLKVTE LMLDEAPHEL EGLAVEGDAA LKQLAELKAL QTLTEYAGDL LEGQNQIVQR VNDFVDSNPV YLLDQPLREE A RWNLLPEM ...String:
MLRQVVRRSN PLRMQVRGSA WNFQELMESR IPDYKGRPNR SGAELEQVKA ALPKIEFMTS YEFDVLTKTR SNLTKEYSYQ RDMRLKVTE LMLDEAPHEL EGLAVEGDAA LKQLAELKAL QTLTEYAGDL LEGQNQIVQR VNDFVDSNPV YLLDQPLREE A RWNLLPEM DHKTRSLVRT ELRDWLPAEY RQTRAVDLQQ VAAFSPPVKA DMFRAIEARA KDAEAEIRSL PPAEQAGLLA LV KDNVAKS KAFIDPTYDI TPEAINACND VDALRAMAHR VTEYSGDARL LAIYGKAAQL TGDTAAQAIL KEAKDLVF

+
Macromolecule #29: COXEG9

MacromoleculeName: COXEG9 / type: protein_or_peptide / ID: 29 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 31.754857 KDa
SequenceString: MMNKGRILLG TNPGDIALNS KRFTVGKFVA WACGGWGLKD WIFPSLFIGR GDGPDFDRIV KHTLQSSSAI EKVNWFDSPF ACYTEWFVE HFPGFFDSRY RFEMSAKTIL ANKYPIKDFP VVDMRSWRSS RLFDLFEVPH PEHTFVFGGP VLLNTEAKRA E RLEQEWHG ...String:
MMNKGRILLG TNPGDIALNS KRFTVGKFVA WACGGWGLKD WIFPSLFIGR GDGPDFDRIV KHTLQSSSAI EKVNWFDSPF ACYTEWFVE HFPGFFDSRY RFEMSAKTIL ANKYPIKDFP VVDMRSWRSS RLFDLFEVPH PEHTFVFGGP VLLNTEAKRA E RLEQEWHG KDGTFVDVHP LNVATESHTE VSVIGGIKVY NGVWQGGKDS WKRDSAKPEL TAPFHSPIWY RNMFIVKNAD QL VEHFGEN LSDETWQEVR KEHLAFHERF HKDYSFA

+
Macromolecule #30: COX7a

MacromoleculeName: COX7a / type: protein_or_peptide / ID: 30 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.078975 KDa
SequenceString:
MLSRLLHGPG SDKGHGYFHP DHGLVDSAAQ NIRGPYWHAE NMQFMQQTTQ SGEKLPVPLT ETAAQSSKLP VLSAQDGKTL QKIQLTDGS KVPKAATLVK WNPKSVHQWH SDDILRVDMT KHPEWVRTMR MFHGTVWRHR PEFRHPWFSR GSRASGIIML V FGAVAYGE ITFGKRLGGV

+
Macromolecule #31: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 31 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #32: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 32 / Number of copies: 15 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #33: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 33 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #34: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 34 / Number of copies: 22 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

+
Macromolecule #35: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 35 / Number of copies: 3 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

+
Macromolecule #36: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 36 / Number of copies: 11 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #37: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 37 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

+
Macromolecule #38: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 38 / Number of copies: 6 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

+
Macromolecule #39: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 39 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #40: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 40 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #41: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 41 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #42: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}p...

MacromoleculeName: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
type: ligand / ID: 42 / Number of copies: 2 / Formula: S12
Molecular weightTheoretical: 523.597 Da
Chemical component information

ChemComp-S12:
O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMTrisTrimethylsilyl
100.0 mMNaClSodium chlorideSodium chloride
0.002 %PMSFPhenylmethylsulfonyl fluoridePMSF
0.1 %GDNGlyco-diosgenin
1.0 mMEDTAEthylenediaminetetraacetic acidEthylene diamine tetraacetic acid

Details: SEC buffer (30 mM Tris pH 7.4, 100 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v), 1mM EDTA)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9807 / Average exposure time: 7.8 sec. / Average electron dose: 51.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3232325
Startup modelType of model: INSILICO MODEL
In silico model: 3D ab-inito model reconstruction in cryosparc
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. v.3.3.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 45074 / Software - Name: cryoSPARC (ver. v.3.3.2)
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. v.3.3.2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.3.3.2) / Number images used: 135598
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8iuj:
Cryo-EM structure of Euglena gracilis super-complex III2+IV2, composite

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