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- PDB-9fzl: Perkinsus marinus respiratory supercomplex CII2CIII2CIV2 in an in... -

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Basic information

Entry
Database: PDB / ID: 9fzl
TitlePerkinsus marinus respiratory supercomplex CII2CIII2CIV2 in an intermediate state
Components
  • (Cytochrome c oxidase subunit ...) x 20
  • (Succinate dehydrogenase [ubiquinone] ...) x 2
  • (Ubiquinol-cytochrome c ...) x 3
  • Alpha-MPP
  • Amino acid transporter transmembrane domain-containing protein
  • Aurora kinase
  • Cu-binding protein
  • Cytochrome Coxidase subunit, putative
  • Cytochrome b
  • Cytochrome c oxidase polypeptide II
  • DUF6827 domain-containing protein
  • GINS subunit domain-containing protein
  • Iso-1-cytochrome c
  • Kinesin-like protein
  • Merozoite surface protein, putative
  • Mitochondrial processing peptidase beta subunit
  • Peptidase M14 carboxypeptidase A domain-containing protein
  • QCR10
  • QCR8
  • QCR9
  • Rab-GAP TBC domain-containing protein
  • SDHG
  • SDHH
  • SDHI
  • Syntaxin-1A
  • Transmembrane protein
  • Ubiquitin, putative
KeywordsMEMBRANE PROTEIN / Respiratory supercomplex / CII2CIII2CVI2 / intermediate state
Function / homology
Function and homology information


L-amino acid transmembrane transporter activity / DNA strand elongation involved in mitotic DNA replication / GINS complex / respiratory chain complex III / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / metallocarboxypeptidase activity / electron transfer activity / non-specific serine/threonine protein kinase ...L-amino acid transmembrane transporter activity / DNA strand elongation involved in mitotic DNA replication / GINS complex / respiratory chain complex III / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / metallocarboxypeptidase activity / electron transfer activity / non-specific serine/threonine protein kinase / mitochondrial inner membrane / copper ion binding / protein serine/threonine kinase activity / heme binding / proteolysis / extracellular space / zinc ion binding / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Domain of unknown function (DUF6827) / Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A ...: / Domain of unknown function (DUF6827) / Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Cytochrome b-c1 complex, subunit 6 / Aurora kinase / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c1 / Cytochrome C1 family / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c-like domain superfamily / Cupredoxin / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : ...CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PEROXIDE ION / IRON/SULFUR CLUSTER / Ubiquinone-8 / Uncharacterized protein / Ubiquitin, putative / Peptidase M14 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Merozoite surface protein, putative / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putative / DUF6827 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Aurora kinase / Uncharacterized protein / GINS subunit domain-containing protein / Amino acid transporter transmembrane domain-containing protein / Cytochrome c oxidase polypeptide II / Uncharacterized protein / Uncharacterized protein / Ubiquinol-cytochrome C reductase complex 14kD subunit, putative
Similarity search - Component
Biological speciesPerkinsus marinus (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWu, F. / Amunts, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
CitationJournal: To Be Published
Title: Perkinsus marinus respiratory supercomplex CII2CIII2CIV2 in an intermediate state
Authors: Wu, F. / Amunts, A.
History
DepositionJul 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2M: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
2N: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
2O: SDHG
2P: Transmembrane protein
2Q: Kinesin-like protein
2R: SDHH
2S: DUF6827 domain-containing protein
2T: Rab-GAP TBC domain-containing protein
2U: Syntaxin-1A
2V: SDHI
3A: Mitochondrial processing peptidase beta subunit
3B: Alpha-MPP
3C: Iso-1-cytochrome c
3D: QCR8
3E: QCR9
3F: QCR10
3G: Cytochrome b
3H: Ubiquinol-cytochrome c reductase, iron-sulfur subunit, putative
3I: Ubiquinol-cytochrome C reductase complex 14kD subunit, putative
3J: Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putative
3K: Cu-binding protein
3L: Aurora kinase
40: Cytochrome c oxidase subunit 3
4A: Cytochrome c oxidase subunit 6B
4B: Peptidase M14 carboxypeptidase A domain-containing protein
4C: Cytochrome c oxidase subunit 40
4D: Cytochrome c oxidase subunit 34
4E: Merozoite surface protein, putative
4F: Ubiquitin, putative
4G: Cytochrome c oxidase subunit 33
4H: Cytochrome c oxidase subunit 30
4I: Cytochrome c oxidase subunit 6C
4J: Cytochrome c oxidase subunit 24
4K: Cytochrome c oxidase subunit 37
4L: Cytochrome c oxidase subunit 7A
4M: Cytochrome c oxidase subunit 35
4N: Cytochrome c oxidase polypeptide II
4O: GINS subunit domain-containing protein
4P: Cytochrome c oxidase subunit 2A
4Q: Cytochrome c oxidase subunit 1
4R: Cytochrome c oxidase subunit 32
4S: Cytochrome c oxidase subunit 7C
4T: Cytochrome c oxidase subunit 13
4U: Amino acid transporter transmembrane domain-containing protein
4V: Cytochrome c oxidase subunit 4
4W: Cytochrome c oxidase subunit 19
4X: Cytochrome Coxidase subunit, putative
4Y: Cytochrome c oxidase subunit 18
4Z: Cytochrome c oxidase subunit 31
2m: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
2n: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
2o: SDHG
2p: Transmembrane protein
2q: Kinesin-like protein
2r: SDHH
2s: DUF6827 domain-containing protein
2t: Rab-GAP TBC domain-containing protein
2u: Syntaxin-1A
2v: SDHI
3a: Mitochondrial processing peptidase beta subunit
3b: Alpha-MPP
3c: Iso-1-cytochrome c
3d: QCR8
3e: QCR9
3f: QCR10
3g: Cytochrome b
3h: Ubiquinol-cytochrome c reductase, iron-sulfur subunit, putative
3i: Ubiquinol-cytochrome C reductase complex 14kD subunit, putative
3j: Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putative
3k: Cu-binding protein
3l: Aurora kinase
41: Cytochrome c oxidase subunit 3
4a: Cytochrome c oxidase subunit 6B
4b: Peptidase M14 carboxypeptidase A domain-containing protein
4c: Cytochrome c oxidase subunit 40
4d: Cytochrome c oxidase subunit 34
4e: Merozoite surface protein, putative
4f: Ubiquitin, putative
4g: Cytochrome c oxidase subunit 33
4h: Cytochrome c oxidase subunit 30
4i: Cytochrome c oxidase subunit 6C
4j: Cytochrome c oxidase subunit 24
4k: Cytochrome c oxidase subunit 37
4l: Cytochrome c oxidase subunit 7A
4m: Cytochrome c oxidase subunit 35
4n: Cytochrome c oxidase polypeptide II
4o: GINS subunit domain-containing protein
4p: Cytochrome c oxidase subunit 2A
4q: Cytochrome c oxidase subunit 1
4r: Cytochrome c oxidase subunit 32
4s: Cytochrome c oxidase subunit 7C
4t: Cytochrome c oxidase subunit 13
4u: Amino acid transporter transmembrane domain-containing protein
4v: Cytochrome c oxidase subunit 4
4w: Cytochrome c oxidase subunit 19
4x: Cytochrome Coxidase subunit, putative
4y: Cytochrome c oxidase subunit 18
4z: Cytochrome c oxidase subunit 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,028,628260
Polymers1,880,15798
Non-polymers148,472162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Succinate dehydrogenase [ubiquinone] ... , 2 types, 4 molecules 2M2m2N2n

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial


Mass: 65705.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial


Mass: 29680.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: succinate dehydrogenase

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Protein , 22 types, 44 molecules 2O2o2P2p2Q2q2R2r2S2s2T2t2V2v3A3a3B3b3C3c3D3d3E3e3F3f3G3g3K3k...

#3: Protein SDHG


Mass: 17795.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KTH2
#4: Protein Transmembrane protein


Mass: 18583.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#5: Protein Kinesin-like protein


Mass: 8005.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#6: Protein SDHH


Mass: 13456.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#7: Protein DUF6827 domain-containing protein / SDHE


Mass: 18889.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L1Y6
#8: Protein Rab-GAP TBC domain-containing protein


Mass: 9878.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#10: Protein SDHI


Mass: 10148.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LCL6
#11: Protein Mitochondrial processing peptidase beta subunit


Mass: 51513.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#12: Protein Alpha-MPP


Mass: 55322.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#13: Protein Iso-1-cytochrome c / CytC1


Mass: 27275.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5K8N0
#14: Protein QCR8


Mass: 11763.454 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L848
#15: Protein QCR9


Mass: 11417.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#16: Protein QCR10


Mass: 10329.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KTV6
#17: Protein Cytochrome b


Mass: 42452.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#21: Protein Cu-binding protein


Mass: 8656.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#22: Protein Aurora kinase


Mass: 7793.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
References: UniProt: C5LDF5, non-specific serine/threonine protein kinase
#25: Protein Peptidase M14 carboxypeptidase A domain-containing protein / COX36 / Cytochrome c oxidase subunit 36


Mass: 10475.341 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KED7
#28: Protein Merozoite surface protein, putative / COX6A / Cytochrome c oxidase subunit 6A


Mass: 18761.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0U1
#29: Protein Ubiquitin, putative / COX39 / Cytochrome c oxidase subunit 39


Mass: 8624.899 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KBY9
#37: Protein Cytochrome c oxidase polypeptide II / COX2B / Cytochrome c oxidase subunit 2B


Mass: 14594.835 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LND1
#44: Protein Amino acid transporter transmembrane domain-containing protein / COX38 / Cytochrome c oxidase subunit 38


Mass: 10665.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG64
#47: Protein Cytochrome Coxidase subunit, putative


Mass: 26522.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

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Protein/peptide , 2 types, 4 molecules 2U2u4O4o

#9: Protein/peptide Syntaxin-1A


Mass: 5534.095 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#38: Protein/peptide GINS subunit domain-containing protein / COX2C / Cytochrome c oxidase subunit 2C


Mass: 5427.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG07

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Ubiquinol-cytochrome c ... , 3 types, 6 molecules 3H3h3I3i3J3j

#18: Protein Ubiquinol-cytochrome c reductase, iron-sulfur subunit, putative


Mass: 37320.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#19: Protein Ubiquinol-cytochrome C reductase complex 14kD subunit, putative / QCR7


Mass: 20940.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LWC5
#20: Protein Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putative / QCR6


Mass: 10852.286 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0W9

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Cytochrome c oxidase subunit ... , 20 types, 40 molecules 40414A4a4C4c4D4d4G4g4H4h4I4i4J4j4K4k4L4l4M4m4P4p4Q4q4R4r4S4s...

#23: Protein Cytochrome c oxidase subunit 3


Mass: 28167.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#24: Protein Cytochrome c oxidase subunit 6B


Mass: 12040.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#26: Protein Cytochrome c oxidase subunit 40 / COX40


Mass: 8828.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L7H1
#27: Protein Cytochrome c oxidase subunit 34


Mass: 11072.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#30: Protein Cytochrome c oxidase subunit 33 / COX33


Mass: 12070.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KJE7
#31: Protein Cytochrome c oxidase subunit 30


Mass: 15972.974 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#32: Protein Cytochrome c oxidase subunit 6C / COX6C


Mass: 23967.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPW2
#33: Protein Cytochrome c oxidase subunit 24


Mass: 21376.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#34: Protein Cytochrome c oxidase subunit 37 / COX37


Mass: 10228.065 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KST9
#35: Protein Cytochrome c oxidase subunit 7A / COX7A


Mass: 15282.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KPD1
#36: Protein Cytochrome c oxidase subunit 35 / COX35


Mass: 10932.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LDS7
#39: Protein Cytochrome c oxidase subunit 2A


Mass: 21273.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#40: Protein Cytochrome c oxidase subunit 1


Mass: 52063.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: cytochrome-c oxidase
#41: Protein Cytochrome c oxidase subunit 32 / COX32


Mass: 12904.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KSX3
#42: Protein Cytochrome c oxidase subunit 7C / COX7C


Mass: 7711.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPK3
#43: Protein Cytochrome c oxidase subunit 13


Mass: 14001.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#45: Protein Cytochrome c oxidase subunit 4


Mass: 21719.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#46: Protein Cytochrome c oxidase subunit 19 / COX19


Mass: 16881.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0W2
#48: Protein Cytochrome c oxidase subunit 18


Mass: 12898.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#49: Protein Cytochrome c oxidase subunit 31


Mass: 22296.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

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Non-polymers , 19 types, 162 molecules

#50: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#51: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe2S2
#52: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4
#53: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe3S4
#54: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#55: Chemical...
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#56: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#57: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#58: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C49H74O4
#59: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#60: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#61: Chemical ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C56H92O29 / Comment: detergent*YM
#62: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#63: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu2
#64: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu
#65: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#66: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C49H56FeN4O6
#67: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: O2
#68: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: respiratory supercomplex / Type: COMPLEX / Entity ID: #1-#49 / Source: NATURAL
Source (natural)Organism: Perkinsus marinus (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296890
Details: Resolution items should not be applied to composite map. Here, resolution value provided is the average of focused refined maps.
Symmetry type: POINT

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