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- EMDB-11877: Cryo-EM structure of Polytomella Complex-I (membrane arm) -

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Basic information

Entry
Database: EMDB / ID: EMD-11877
TitleCryo-EM structure of Polytomella Complex-I (membrane arm)
Map data
Sample
  • Complex: Polytomella complex I - Membrane arm
    • Protein or peptide: x 35 types
  • Ligand: x 5 types
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsKlusch N / Kuehlbrandt W / Yildiz O
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ar9
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11877.png

Downloads & links

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Map

FileDownload / File: emd_11877.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.045768026 - 0.08298486
Average (Standard dev.)5.8371395e-05 (±0.0013974007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 502.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z502.200502.200502.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0460.0830.000

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Supplemental data

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Half map: #2

Fileemd_11877_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_11877_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 : Polytomella complex I - Membrane arm

EntireName: Polytomella complex I - Membrane arm
Components
  • Complex: Polytomella complex I - Membrane arm
    • Protein or peptide: ND3
    • Protein or peptide: ND1
    • Protein or peptide: ND6
    • Protein or peptide: ND4L
    • Protein or peptide: ND5
    • Protein or peptide: ND4
    • Protein or peptide: ND2
    • Protein or peptide: C1-FDX
    • Protein or peptide: SDAP1
    • Protein or peptide: PGIV
    • Protein or peptide: B14.7
    • Protein or peptide: B16.6
    • Protein or peptide: MWFE
    • Protein or peptide: B9
    • Protein or peptide: KFYI
    • Protein or peptide: B14.5b
    • Protein or peptide: 15 kDa
    • Protein or peptide: MNLL
    • Protein or peptide: ESSS
    • Protein or peptide: NUOP4
    • Protein or peptide: NUOP5
    • Protein or peptide: AGGG
    • Protein or peptide: B12
    • Protein or peptide: ASHI
    • Protein or peptide: B15
    • Protein or peptide: B22
    • Protein or peptide: B18
    • Protein or peptide: PDSW
    • Protein or peptide: NUOP7
    • Protein or peptide: NUOP8
    • Protein or peptide: unknown
    • Protein or peptide: unknown
    • Protein or peptide: CAL
    • Protein or peptide: CA2
    • Protein or peptide: CA3
  • Ligand: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CARDIOLIPIN
  • Ligand: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
  • Ligand: water

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Supramolecule #1: Polytomella complex I - Membrane arm

SupramoleculeName: Polytomella complex I - Membrane arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)

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Macromolecule #1: ND3

MacromoleculeName: ND3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 17.8286 KDa
SequenceString:
MQKRTLYNAM TPAQRYFVEG EHVVQAEANR DILFTQLDSN SYLPVLHYVL VGTALGVVFL VLPLLIAPAR VDLDKISAYE CGFDAFGEA RETFSVSFYI VSIMYLLFDI EVVYLIPYVM TNATEYMYWV MQTFVAILVG GFFYEWRMGA LEWRE

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Macromolecule #2: ND1

MacromoleculeName: ND1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 31.829836 KDa
SequenceString: MNLNIIMTVL PLLVSVAFLT LSERAVMGSL QRRMGPAVSG AFGILQPFWD GFKLAVKEPI LPANAAAGIF YAAPLICICI CVASWCTLL LTDLSIGGLF LLLLSSLAVY GVLLAGYSCN SKYAFLGCLR SVSLMISYEL VISVVILCVI LETRDGNGFP C LNLTETAS ...String:
MNLNIIMTVL PLLVSVAFLT LSERAVMGSL QRRMGPAVSG AFGILQPFWD GFKLAVKEPI LPANAAAGIF YAAPLICICI CVASWCTLL LTDLSIGGLF LLLLSSLAVY GVLLAGYSCN SKYAFLGCLR SVSLMISYEL VISVVILCVI LETRDGNGFP C LNLTETAS QTKIILIPAG LLFYICSLAE SKRVPFDLPE AEAELVAGYN VEYSSLGFAV FFVAEYGNTL LMAALINIYF LG KLNSALI AAIFVSFIWV RGTLPRYRYD MFMQIGWKSL LPVALALYLA QASLGY

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Macromolecule #3: ND6

MacromoleculeName: ND6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 15.938104 KDa
SequenceString:
MLLIYIMLSN IVVLALSVVL TSSPFMALMY SILLYLNVQT ILWSLGYDFM ALIYALVYVG ALAVLFLFVV MMVRIQVSTL STKTIQSVL SWLAIILIFS YGDVSFSFPC GAESLLNFGT QLYSSCSDLT LLNSLALTIA LFGSLV

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Macromolecule #4: ND4L

MacromoleculeName: ND4L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.836075 KDa
SequenceString:
MLSSVVAPQQ PLSIAQPFAV RGYHNDAEFL GAVYNFSIRS VFITGILGAV YWRRNLITML LCSEIAFIAC SVNFLYASAY LNDMAGMLF SITITTISAC ETALGLALCV GYFQSRAANE VEALNLLK

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Macromolecule #5: ND5

MacromoleculeName: ND5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 58.317352 KDa
SequenceString: MFLLAVYFLF FSAIANGFFG RYLGVRGSQL LGPSALFLAL LCSGTIFYEV CIQGCSTNIK LFENFVYSNE LNVSASFLYD PLAATMTLT VVWISCAVHA YQNLYMRGDG SQTLFTSYLS AFTGFMLILV AGQNLVMLFI GWEGIGVCSY LLIGYYGSRV S AVKSANKS ...String:
MFLLAVYFLF FSAIANGFFG RYLGVRGSQL LGPSALFLAL LCSGTIFYEV CIQGCSTNIK LFENFVYSNE LNVSASFLYD PLAATMTLT VVWISCAVHA YQNLYMRGDG SQTLFTSYLS AFTGFMLILV AGQNLVMLFI GWEGIGVCSY LLIGYYGSRV S AVKSANKS LIVNKISDGF LLGSMLYLWF YTGSFSYCSL ATFQIPDVVS ILVLLGAIGK SSQLFFHVWL ADAMEGPTPV SA LIHAATL VTAGIYVLCK LNLHSQSAVG ILGAATALMG GLFGLAANDL KRVIAFSTCS QLGYMMAVLS TCDDGADFAM GHL VSHAGF KATLFLSAGL SIAKENNNFL NRYGSRQGSP TLSFATTIAS LNLLGFPELG GFYSKESILN NAYINQGVSI ILTL ATFLT AFYTSKVLAQ LYLFPYGNGR QQKSFDIDAT TLICFGLLLS EMLLRIFTGS SLSQNMTTNL PAHIKNLPFW VALSG ALSG LATTNLFSSN FMRFFGNRGG FDVFYARKCS NVFYHNAYVS YTLLDRGFLK LY

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Macromolecule #6: ND4

MacromoleculeName: ND4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 48.407109 KDa
SequenceString: MSLYLFMLFL QPLSLSFVSR SFSKISSLMM SFATLWSAVY MWFTSNGANQ TFYQVVSWGS DWSTFGVCYT SLYISLLCAF IFPICVILV QGYRALSILI CIQTAVSLSI VSLHMLAFYA LFESSLLLFF ILIGRRKYGS LSAAYNISIY TFISALGFLI S AFWLNWSF ...String:
MSLYLFMLFL QPLSLSFVSR SFSKISSLMM SFATLWSAVY MWFTSNGANQ TFYQVVSWGS DWSTFGVCYT SLYISLLCAF IFPICVILV QGYRALSILI CIQTAVSLSI VSLHMLAFYA LFESSLLLFF ILIGRRKYGS LSAAYNISIY TFISALGFLI S AFWLNWSF GSVCALLPNE EANSFVAFGI FILLWVKAPL VPFHLWLPEA HVYAPTAGSV LLAGVLLKIS IVGLHVFFLP IC ASSIVKA FPLILSICLG SFIFSSFSTL KQIDLKKIVA YSSISHMAIV FLSSATNSGL GIQGAVLYCI AHGLISPGLF LLV GILYKN TNTKLVFYLR GLSQQAPVWW SVWVFFMLGN LAFPLFPNFI AEVVCLSALF KNHELYAYAF IFFSFVGTVY SSTV LGRLK GGVSSQCVDA SRLDVISWNP LVLATVVTGI GYM

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Macromolecule #7: ND2

MacromoleculeName: ND2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 41.939418 KDa
SequenceString: MWENLWYLDI LINVLIITIF GLISCSSSAT KSYDLKGCFI ISMVGGVYDI PSAILWCLAS LSILNFNGFF ASLFLVFTWI SNLFAMQSL NFLGIYLAFE MQSLCLLVLG KITANENQRW FAYRGLLKYL VLSLIAGSIF IFHASSSYLQ SGVMISDSLV T YVFLLFKL ...String:
MWENLWYLDI LINVLIITIF GLISCSSSAT KSYDLKGCFI ISMVGGVYDI PSAILWCLAS LSILNFNGFF ASLFLVFTWI SNLFAMQSL NFLGIYLAFE MQSLCLLVLG KITANENQRW FAYRGLLKYL VLSLIAGSIF IFHASSSYLQ SGVMISDSLV T YVFLLFKL GVAPFHMYTL ELFSVVSRHV AFVFSTLPKL SVLYLISNSN IGSECVWWGL ISLWLGSISQ YQSVFVRSIL LY SSVAEIG LVLLVLQEGF SWEAFSWVSI YFLSLSGVWH ANSKFVSAIS VASIAGLPPF LGFIGKAQIL KSLVSINLGI LIF SSILAA TISFIGYLRL IRLMYLVSPV KWKNNKDSSF INWSTWMLTV GTLPMVYSV

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Macromolecule #8: C1-FDX

MacromoleculeName: C1-FDX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 23.115135 KDa
SequenceString: MALLRALAKP LRSLQAVSSV AQVSLRQFGA ASHHDDHHDD HDHYTPPKTV FEDTITINVL DYDGKKHAVK ALIGTPLNKA LVEYGFSST YFFPNMGYYT QHISDAHVFI PEEYWKYVEN VDLKTDDAEA IKLMFKLVVQ DYQRETSFFA SYLTLNKEMD N MTIGFGPI ...String:
MALLRALAKP LRSLQAVSSV AQVSLRQFGA ASHHDDHHDD HDHYTPPKTV FEDTITINVL DYDGKKHAVK ALIGTPLNKA LVEYGFSST YFFPNMGYYT QHISDAHVFI PEEYWKYVEN VDLKTDDAEA IKLMFKLVVQ DYQRETSFFA SYLTLNKEMD N MTIGFGPI KPWHITPKWS FNGHHNVKDR MFDRLETGPF IE

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Macromolecule #9: SDAP1

MacromoleculeName: SDAP1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.409164 KDa
SequenceString:
MALSSASSFF KAVVLRNLRV SVSQSTFVPI GNVISRAYGG HGLDRDTVTE RVIHVAKHFE KVDPNKITPT ATFEELGLDS LDTVELVMA LEEEFGLEIP DNEADKITTM ADAISYVVSN PLAK

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Macromolecule #10: PGIV

MacromoleculeName: PGIV / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 11.758452 KDa
SequenceString:
MVARVPYSHE LYAMAKHIVF RNEKEHNAIL ECKAQHDWPE DCKPESEAIV RATNKLFQDI MQKAPEEFKD YAKCLDWYGL KFSKCREKQ AAFEAAFPLS E

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Macromolecule #11: B14.7

MacromoleculeName: B14.7 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 22.521609 KDa
SequenceString: MTFNYVIPYG GSSSYTINNE PVKAEEVTVD FSKEPSASSL KLADKSDWIA YTFNNVPLMA TVGLLAGAHE AFLHYERTPI YGKRTYNII KKLAPIVINK TAYATLLGAI FCATDALYEN YSGKKSYTSG MVAGAATGAV FAIGRPLPQP LVWPLVFAAA P VIADLFGE ...String:
MTFNYVIPYG GSSSYTINNE PVKAEEVTVD FSKEPSASSL KLADKSDWIA YTFNNVPLMA TVGLLAGAHE AFLHYERTPI YGKRTYNII KKLAPIVINK TAYATLLGAI FCATDALYEN YSGKKSYTSG MVAGAATGAV FAIGRPLPQP LVWPLVFAAA P VIADLFGE VYPESMKSAR GYGTPYGFEN LDDAVPTRNP IRRNPHHY

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Macromolecule #12: B16.6

MacromoleculeName: B16.6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 16.261724 KDa
SequenceString:
MTEFVNRGFP GLKSIKDLPK VQDVPPPGGF PSIRIERKLP NTGPTGLAVF LGFTAFMALA VNQARDRKST NRLEAEEVYT ARSILHPIL QAEWDLRYLE HQRKEREDEA KIMKDVPGWK VGEATSRRRW LPPVESFDVR PLI

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Macromolecule #13: MWFE

MacromoleculeName: MWFE / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 8.504547 KDa
SequenceString:
MGWYALPSYV IVSAAWAAGF WAIDTYQIYK EGKPSWNQNK DQFQRALYRR DWYLRREQET IGMFLGFDYG A

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Macromolecule #14: B9

MacromoleculeName: B9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 4.613678 KDa
SequenceString: (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) ...String:
(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #15: KFYI

MacromoleculeName: KFYI / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 12.554098 KDa
SequenceString:
MGGHDHHHPS VPEPPYAKYL ANKSHYCPPD FHYSREIYAP YGGYFNDPKG WRTNTAIATL VMLAGAYAVF CFGNAREERL RAPKGWIPS QLWNDNVPTP VDYRGKVLKD E

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Macromolecule #16: B14.5b

MacromoleculeName: B14.5b / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 9.574958 KDa
SequenceString:
MGWEYAGTYG ALCGMVYAIG SNVISGRAWF RRPWVHVTSV TLSYLGSKLL DEVQDTYYLE HLKRVERKGL QVTEEHKKLF SAY

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Macromolecule #17: 15 kDa

MacromoleculeName: 15 kDa / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 8.915221 KDa
SequenceString:
MSGFGLQSGT ARCYDWYMDY LKCMDESKAP MITLRKQECS EWLEDYNECL HRDKLKLRKL LIEREKNKQE AASSS

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Macromolecule #18: MNLL

MacromoleculeName: MNLL / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.507196 KDa
SequenceString:
MTWPKPINPY DVPSSPAYHR LQEPSYPVID KDPDFWTAVS NVRKEEWGTT AAVAAGTFVM GYYLGAKGHT GKASAYFTSF LATKSITLY HAYNSADRLM GFKENSREVV KNVPAALVPE HY

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Macromolecule #19: ESSS

MacromoleculeName: ESSS / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 19.333246 KDa
SequenceString:
MNRIPALRRI GAQALRNPVT RAGGASGHPN GSFWSEGTQV GLNGFKYGEI PLPNGQPRKK LWLENIWNIG YGGFFLGAFC LYYGAPPGH VIPSQWATPK AKDEYAVDMK MIDKYNERPD LQARLSIVLK DLNMIEEEAY DLIMMRKDYK VLLGLHSGRV P ADLKAIYE ELEA

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Macromolecule #20: NUOP4

MacromoleculeName: NUOP4 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 9.145251 KDa
SequenceString:
MAGGNYASLK ADTSMDHVFG DSTNKLNYDF QLMSSKEAFF WNYTLYPIVG FPIFLYLYQF NKLENFEAEI AAAKAAKAAS E

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Macromolecule #21: NUOP5

MacromoleculeName: NUOP5 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 15.118817 KDa
SequenceString:
MFFFEFLQGK ISDSQKEVDS QAEWYAEYDK LEKARQKRRI WKWRDSDSRD EYAINAEEPV IYIRSSLFGR TEVDPTGKNT NRNHQYLYN LKVLGHKTYT RRDPNELQKA QAEVDTLSAA GRLGPLSPF

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Macromolecule #22: AGGG

MacromoleculeName: AGGG / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 7.42214 KDa
SequenceString: (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) ...String:
(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)(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)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #23: B12

MacromoleculeName: B12 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 6.332208 KDa
SequenceString:
MSSKIGFQWE KYEAWRYHPL LRFNKNTMFP GVGLGAAAFA VYYVVDTLSG DKSHH

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Macromolecule #24: ASHI

MacromoleculeName: ASHI / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 16.986572 KDa
SequenceString:
MSLTLGLRSL SRGALAARNA LPKRAGAGGP VKLSPPVDKP LPYNYDFWMD NGIYPGQPIY DGMFGSMVGN MSLEYMAKGW LVLLPILSA PFVYEHCIAD DVTRNPFVPR QYPSEVREFL ALFKNGFVLN DYSQPDYEEM KRRQSGLLTP IY

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Macromolecule #25: B15

MacromoleculeName: B15 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 16.27623 KDa
SequenceString:
MSALQAVKNL TTRMRPFAFQ QIRKASNSSR IAGDTTGKYT PNIFSPETPM DRSFSHVPKN PFWEAWVFRR DNIQREFVWT WQTIFDLAT FVGGLYVAMY ATASFCSRQN DKRNGYPERN YYFSDSKSNF VIPDEREFY

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Macromolecule #26: B22

MacromoleculeName: B22 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 14.418621 KDa
SequenceString:
MASEAVLRLP HKLRVMRMYR TGLKEIVNWS YGRHEFYPRA NALRMEFEAN KELSDREQIR KLVLHGEDLL ARFRHWEPTI RSEFVGGTV YGVWPQHCKD VKFVPNPAYI DEFKQGDTVL LY

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Macromolecule #27: B18

MacromoleculeName: B18 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 10.292997 KDa
SequenceString:
MADRFPPPKM VATQEEMDNA DIPYKYRDYC AHLIIDFKEC RYGHPLTWRI NCAHELHHYN KCSYIEFKRR VAIAIEEKKR RGLMV

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Macromolecule #28: PDSW

MacromoleculeName: PDSW / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 18.43491 KDa
SequenceString:
MTTATIEERR AFHKEVLDIV QSKLANKNSE WARPEEPILH NLKSEKEEPH VYYHNNNFRV TRQLIHFEKT KIFEDELDKC MRTHGEAKY RKCQEIAKRF QASCRVASNL ERGPNARKRD VGFIYQNNKL RELEKDAKEL GLNNPFPPSS PRTTIGY

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Macromolecule #29: NUOP7

MacromoleculeName: NUOP7 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.476524 KDa
SequenceString:
MVKTLADYIH WRNKPSSIPP VDEYRPPVPL VNYDKLSTQF FSKLDNDPVI NRVLRAPKVT VMATSLPIVN HPAFLFVAGA LTGFSLTYA ITSHYVGRKE IENLVKFDPR YFPEYTKSS

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Macromolecule #30: NUOP8

MacromoleculeName: NUOP8 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 15.743896 KDa
SequenceString:
MRSALRLANA TRLSTFRLTS APAVRLASPS FFVQKEDEEN TRSIHTSNSS FHDEPKHQIP GNALDNWAFL RTYAKPLPDM IHYYYYVYL FGFFFVYKVA DFPEYSPRVL VMAALIGSLF YVRRDWVHRE FKDSP

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Macromolecule #31: unknown

MacromoleculeName: unknown / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 4.273259 KDa
SequenceString: (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) ...String:
(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #32: unknown

MacromoleculeName: unknown / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 3.507314 KDa
SequenceString:
(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 #33: CAL

MacromoleculeName: CAL / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 31.34842 KDa
SequenceString: MLRRGAKELV QLLRTPVKQG AQLQYVATRN VNFYDAPNGP AVEQVKIEDE WYNRQRTEFN ILNKQPSKAD DVFIAPNAVV CGDVDLYQK VSIFFGAVVR GDLNTIRIGE NSTILDKAVV HAASTSPTGL NAATIIGSNV TVEPHAVLRS CRIGDNCIVG A RSVVCEGA ...String:
MLRRGAKELV QLLRTPVKQG AQLQYVATRN VNFYDAPNGP AVEQVKIEDE WYNRQRTEFN ILNKQPSKAD DVFIAPNAVV CGDVDLYQK VSIFFGAVVR GDLNTIRIGE NSTILDKAVV HAASTSPTGL NAATIIGSNV TVEPHAVLRS CRIGDNCIVG A RSVVCEGA IMHPESVLAP GSVLAPGRQI PSGELWAGSP AKFVRKLTYY ETSNVIRESA EHYYDIATGF RNETFDHGSA WR DAEAYRQ KLVDYKEYNW VNYREQKYVM RLQRDAAELE KLL

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Macromolecule #34: CA2

MacromoleculeName: CA2 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 33.201867 KDa
SequenceString: MSLLKNYPPS YLYPFRHPKP EGVIEKVLFN LGSLFRSAGQ GMDELGSLML GNGGMQESVG PNLAYAPVKY NPAAAPKAGI VAPIPASAQ RVLGVKEIVL PSKAESTFIA PNANVLGDVK IGAKSSIWYG AVLRGDVNSI EIGDNTNVQD NVTIHVAKHS I DGKLRNTV ...String:
MSLLKNYPPS YLYPFRHPKP EGVIEKVLFN LGSLFRSAGQ GMDELGSLML GNGGMQESVG PNLAYAPVKY NPAAAPKAGI VAPIPASAQ RVLGVKEIVL PSKAESTFIA PNANVLGDVK IGAKSSIWYG AVLRGDVNSI EIGDNTNVQD NVTIHVAKHS I DGKLRNTV IGNNVTIGHC ATIHACTIAD NVIIGMGATV LDGVKVESGS IVGAGSIVPP NTVIPAGQVW VGNPAKFIRN VL PEENGFI ASSANNYDLL GQQHKFENSK VFEEMLVEEE IAKDRELLED KNLAVHQLYI FDPQTQLAAR PRR

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Macromolecule #35: CA3

MacromoleculeName: CA3 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 24.150471 KDa
SequenceString: MASFLKTIVW RCGFAIKETG LALETLGCKL QGNYSFREKC SRHTPLTQYQ FKAPSVGEST FVAPSALVSG DVIIGEKSSV LYNAVVRGE FKSVTIGEGS TISDNAYVGS SSEFSPETVI GSNVSVGSGA VLKGCTVGNN VLIGNNVIIS EKATVEDNTI L APGSYVPE ...String:
MASFLKTIVW RCGFAIKETG LALETLGCKL QGNYSFREKC SRHTPLTQYQ FKAPSVGEST FVAPSALVSG DVIIGEKSSV LYNAVVRGE FKSVTIGEGS TISDNAYVGS SSEFSPETVI GSNVSVGSGA VLKGCTVGNN VLIGNNVIIS EKATVEDNTI L APGSYVPE DVVVKSGELW SGSPAQKLRN LDEKELALFN TLSVGATELA ADHAVIMKLL ELKQKEFIK

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Macromolecule #36: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...

MacromoleculeName: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 36 / Number of copies: 7 / Formula: PC7
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-PC7:
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #37: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 37 / Number of copies: 7 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #38: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 38 / Number of copies: 5 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #39: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
type: ligand / ID: 39 / Number of copies: 1 / Formula: 8Q1
Molecular weightTheoretical: 540.651 Da
Chemical component information

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

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Macromolecule #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 364 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42350
FSC plot (resolution estimation)

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