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- PDB-9fq8: Perkinsus marinus Respiratory complex CIV -

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Basic information

Entry
Database: PDB / ID: 9fq8
TitlePerkinsus marinus Respiratory complex CIV
Components
  • (Cytochrome c oxidase ...) x 18
  • Amino acid transporter transmembrane domain-containing protein
  • Cg8 protein
  • Cytochrome Coxidase subunit, putative
  • Cytochrome oxidase subunit II copper A binding domain-containing protein
  • GINS subunit domain-containing protein
  • Merozoite surface protein, putative
  • Peptidase M14 carboxypeptidase A domain-containing protein
  • Ubiquitin, putative
KeywordsMEMBRANE PROTEIN / Respiratory complex / CIV
Function / homology
Function and homology information


L-amino acid transmembrane transporter activity / DNA strand elongation involved in mitotic DNA replication / GINS complex / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / metallocarboxypeptidase activity / copper ion binding / proteolysis / extracellular space / zinc ion binding / membrane
Similarity search - Function
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 c/quinol oxidase subunit II / Copper centre Cu(A) ...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 c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PEROXIDE ION / Ubiquitin, putative ...CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PEROXIDE ION / Ubiquitin, putative / Peptidase M14 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Merozoite surface protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GINS subunit domain-containing protein / Amino acid transporter transmembrane domain-containing protein / Cytochrome c oxidase polypeptide II / Uncharacterized protein / Uncharacterized protein
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: Biorxiv / Year: 2024
Title: Structure of the II2-III2-IV2 mitochondrial supercomplex from the parasite Perkinsus marinus
Authors: Wu, F. / Muhleip, A. / Gruhl, T. / Sheiner, L. / Marechal, A. / Amunts, A.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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 oxidase subunit II copper A binding domain-containing protein
4Q: Cytochrome c oxidase subunit 1
4R: Cytochrome c oxidase subunit 32
4S: Cytochrome c oxidase subunit 7C
4T: Cytochrome c oxidase 13
4U: Amino acid transporter transmembrane domain-containing protein
4V: Cg8 protein
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)451,67763
Polymers419,46526
Non-polymers32,21337
Water181
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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Cytochrome c oxidase ... , 18 types, 18 molecules 4A4C4D4G4H4I4J4K4L4M4N4Q4R4S4T4W4Y4Z

#1: Protein Cytochrome c oxidase subunit 6B


Mass: 12040.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#3: Protein Cytochrome c oxidase subunit 40 / COX40


Mass: 8828.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L7H1
#4: Protein Cytochrome c oxidase subunit 34 / COX34


Mass: 11072.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#7: Protein Cytochrome c oxidase subunit 33 / COX33


Mass: 12070.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KJE7
#8: Protein Cytochrome c oxidase subunit 30 / COX30


Mass: 15972.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#9: Protein Cytochrome c oxidase subunit 6C / COX6C


Mass: 23967.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPW2
#10: Protein Cytochrome c oxidase subunit 24 / COX24


Mass: 21376.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#11: Protein Cytochrome c oxidase subunit 37 / COX37


Mass: 10228.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KST9
#12: Protein Cytochrome c oxidase subunit 7A / COX7A


Mass: 15282.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KPD1
#13: Protein Cytochrome c oxidase subunit 35 / COX35


Mass: 11003.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#14: Protein Cytochrome c oxidase polypeptide II


Mass: 14594.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LND1
#17: Protein Cytochrome c oxidase subunit 1


Mass: 52063.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: cytochrome-c oxidase
#18: Protein Cytochrome c oxidase subunit 32 / COX32


Mass: 12904.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KSX3
#19: Protein Cytochrome c oxidase subunit 7C / COX7C


Mass: 7711.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPK3
#20: Protein Cytochrome c oxidase 13 / COX13


Mass: 14001.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#23: Protein Cytochrome c oxidase subunit 19 / COX19


Mass: 16881.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0W2
#25: Protein Cytochrome c oxidase subunit 18 / COX18


Mass: 12898.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L2M0
#26: Protein Cytochrome c oxidase subunit 31 / COX31


Mass: 22296.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

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Protein , 7 types, 7 molecules 4B4E4F4P4U4V4X

#2: Protein Peptidase M14 carboxypeptidase A domain-containing protein


Mass: 10475.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KED7
#5: Protein Merozoite surface protein, putative


Mass: 18761.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0U1
#6: Protein Ubiquitin, putative


Mass: 9423.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KBY9
#16: Protein Cytochrome oxidase subunit II copper A binding domain-containing protein


Mass: 21273.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#21: Protein Amino acid transporter transmembrane domain-containing protein


Mass: 10665.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG64
#22: Protein Cg8 protein


Mass: 21719.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#24: Protein Cytochrome Coxidase subunit, putative


Mass: 26522.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

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Protein/peptide , 1 types, 1 molecules 4O

#15: Protein/peptide GINS subunit domain-containing protein


Mass: 5427.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG07

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Non-polymers , 12 types, 38 molecules

#27: 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.: 2 / Source method: isolated from a natural source / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#29: 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.: 14 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#30: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#31: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: Perkinsus marinus Respiratory complex CIV / Type: COMPLEX / Entity ID: #1-#26 / 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 / Symmetry type: POINT

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