9FQ8 | pdb_00009fq8

Perkinsus marinus Respiratory complex CIV

PDB DOI: https://doi.org/10.2210/pdb9FQ8/pdb
EM Map EMD-50363: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Perkinsus marinus
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-06-25
Deposition Author(s): Wu, F., Amunts, A.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Perkinsus marinus Respiratory complex CIV

Wu, F., Amunts, A.

To be published.

Macromolecule Content

Total Structure Weight: 451.68 kDa
Atom Count: 31,410
Modeled Residue Count: 3,569
Deposited Residue Count: 3,569
Unique protein chains: 26

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B	A [auth 4A]	100	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K7H0 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K7H0 Go to UniProtKB: C5K7H0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5K7H0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M14 carboxypeptidase A domain-containing protein	B [auth 4B]	93	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KED7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KED7 Go to UniProtKB: C5KED7
Entity Groups
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UniProt Group	C5KED7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 40	C [auth 4C]	75	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L7H1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L7H1 Go to UniProtKB: C5L7H1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5L7H1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 34	D [auth 4D]	90	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUF4 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUF4 Go to UniProtKB: C5LUF4
Entity Groups
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UniProt Group	C5LUF4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Merozoite surface protein, putative	E [auth 4E]	152	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L0U1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L0U1 Go to UniProtKB: C5L0U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5L0U1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin, putative	F [auth 4F]	80	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KBY9 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KBY9 Go to UniProtKB: C5KBY9
Entity Groups
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UniProt Group	C5KBY9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 33	G [auth 4G]	100	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KJE7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KJE7 Go to UniProtKB: C5KJE7
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UniProt Group	C5KJE7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 30	H [auth 4H]	141	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L104 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L104 Go to UniProtKB: C5L104
Entity Groups
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UniProt Group	C5L104
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I [auth 4I]	196	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LPW2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LPW2 Go to UniProtKB: C5LPW2
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UniProt Group	C5LPW2
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 24	J [auth 4J]	186	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L533 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L533 Go to UniProtKB: C5L533
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UniProt Group	C5L533
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 37	K [auth 4K]	93	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KST9 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KST9 Go to UniProtKB: C5KST9
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UniProt Group	C5KST9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A	L [auth 4L]	122	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KPD1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KPD1 Go to UniProtKB: C5KPD1
Entity Groups
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UniProt Group	C5KPD1
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 35	M [auth 4M]	99	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LDS7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LDS7 Go to UniProtKB: C5LDS7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5LDS7
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide II	N [auth 4N]	131	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K5E4 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K5E4 Go to UniProtKB: C5K5E4
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UniProt Group	C5K5E4
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
GINS subunit domain-containing protein	O [auth 4O]	47	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LG07 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LG07 Go to UniProtKB: C5LG07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5LG07
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome oxidase subunit II copper A binding domain-containing protein	P [auth 4P]	180	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LK31 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LK31 Go to UniProtKB: C5LK31
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UniProt Group	C5LK31
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	Q [auth 4Q]	459	Perkinsus marinus	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for F8SRI9 (Perkinsus marinus ATCC 50439) Explore F8SRI9 Go to UniProtKB: F8SRI9
Entity Groups
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UniProt Group	F8SRI9
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 32	R [auth 4R]	103	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KSX3 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KSX3 Go to UniProtKB: C5KSX3
Entity Groups
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UniProt Group	C5KSX3
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C	S [auth 4S]	65	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L3V7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L3V7 Go to UniProtKB: C5L3V7
Entity Groups
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UniProt Group	C5L3V7
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase 13	T [auth 4T]	121	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K4P8 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K4P8 Go to UniProtKB: C5K4P8
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UniProt Group	C5K4P8
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid transporter transmembrane domain-containing protein	U [auth 4U]	91	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LG64 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LG64 Go to UniProtKB: C5LG64
Entity Groups
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UniProt Group	C5LG64
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Cg8 protein	V [auth 4V]	185	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LR54 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LR54 Go to UniProtKB: C5LR54
Entity Groups
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UniProt Group	C5LR54
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 19	W [auth 4W]	141	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L0W2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L0W2 Go to UniProtKB: C5L0W2
Entity Groups
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UniProt Group	C5L0W2
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome Coxidase subunit, putative	X [auth 4X]	226	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUB2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUB2 Go to UniProtKB: C5LUB2
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UniProt Group	C5LUB2
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 18	Y [auth 4Y]	107	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUI5 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUI5 Go to UniProtKB: C5LUI5
Entity Groups
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UniProt Group	C5LUI5
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 31	Z [auth 4Z]	186	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LYX8 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LYX8 Go to UniProtKB: C5LYX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5LYX8
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Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain BB [auth 4S] SDF format, chain DA [auth 4E] SDF format, chain EA [auth 4E] SDF format, chain EB [auth 4U] SDF format, chain GA [auth 4F] SDF format, chain GB [auth 4W] SDF format, chain IA [auth 4J] SDF format, chain JA [auth 4K] SDF format, chain KB [auth 4Z] SDF format, chain LA [auth 4L] SDF format, chain MA [auth 4M] SDF format, chain OA [auth 4O] SDF format, chain RA [auth 4Q] SDF format, chain SA [auth 4Q] MOL2 format, chain BB [auth 4S] MOL2 format, chain DA [auth 4E] MOL2 format, chain EA [auth 4E] MOL2 format, chain EB [auth 4U] MOL2 format, chain GA [auth 4F] MOL2 format, chain GB [auth 4W] MOL2 format, chain IA [auth 4J] MOL2 format, chain JA [auth 4K] MOL2 format, chain KB [auth 4Z] MOL2 format, chain LA [auth 4L] MOL2 format, chain MA [auth 4M] MOL2 format, chain OA [auth 4O] MOL2 format, chain RA [auth 4Q] MOL2 format, chain SA [auth 4Q] mmCIF format, chain BB [auth 4S] mmCIF format, chain DA [auth 4E] mmCIF format, chain EA [auth 4E] mmCIF format, chain EB [auth 4U] mmCIF format, chain GA [auth 4F] mmCIF format, chain GB [auth 4W] mmCIF format, chain IA [auth 4J] mmCIF format, chain JA [auth 4K] mmCIF format, chain KB [auth 4Z] mmCIF format, chain LA [auth 4L] mmCIF format, chain MA [auth 4M] mmCIF format, chain OA [auth 4O] mmCIF format, chain RA [auth 4Q] mmCIF format, chain SA [auth 4Q]	BB [auth 4S] DA [auth 4E] EA [auth 4E] EB [auth 4U] GA [auth 4F] BB [auth 4S], DA [auth 4E], EA [auth 4E], EB [auth 4U], GA [auth 4F], GB [auth 4W], IA [auth 4J], JA [auth 4K], KB [auth 4Z], LA [auth 4L], MA [auth 4M], OA [auth 4O], RA [auth 4Q], SA [auth 4Q]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth 4S] Focus chain DA [auth 4E] Focus chain EA [auth 4E] Focus chain EB [auth 4U] Focus chain GA [auth 4F] Focus chain GB [auth 4W] Focus chain IA [auth 4J] Focus chain JA [auth 4K] Focus chain KB [auth 4Z] Focus chain LA [auth 4L] Focus chain MA [auth 4M] Focus chain OA [auth 4O] Focus chain RA [auth 4Q] Focus chain SA [auth 4Q] Interactions & Density Focus chain BB [auth 4S] Focus chain DA [auth 4E] Focus chain EA [auth 4E] Focus chain EB [auth 4U] Focus chain GA [auth 4F] Focus chain GB [auth 4W] Focus chain IA [auth 4J] Focus chain JA [auth 4K] Focus chain KB [auth 4Z] Focus chain LA [auth 4L] Focus chain MA [auth 4M] Focus chain OA [auth 4O] Focus chain RA [auth 4Q] Focus chain SA [auth 4Q]
HEA (Subject of Investigation/LOI) Query on HEA Download Ideal Coordinates CCD File SDF format, chain WA [auth 4Q] SDF format, chain XA [auth 4Q] MOL2 format, chain WA [auth 4Q] MOL2 format, chain XA [auth 4Q] mmCIF format, chain WA [auth 4Q] mmCIF format, chain XA [auth 4Q]	WA [auth 4Q], XA [auth 4Q]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain WA [auth 4Q] Focus chain XA [auth 4Q] Interactions & Density Focus chain WA [auth 4Q] Focus chain XA [auth 4Q]
PC1 (Subject of Investigation/LOI) Query on PC1 Download Ideal Coordinates CCD File SDF format, chain FA [auth 4F] MOL2 format, chain FA [auth 4F] mmCIF format, chain FA [auth 4F]	FA [auth 4F]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain FA [auth 4F] Interactions & Density Focus chain FA [auth 4F]
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain AB [auth 4S] SDF format, chain BA [auth 4D] SDF format, chain CA [auth 4E] SDF format, chain FB [auth 4W] SDF format, chain HA [auth 4G] SDF format, chain JB [auth 4Z] SDF format, chain KA [auth 4L] SDF format, chain PA [auth 4Q] SDF format, chain QA [auth 4Q] SDF format, chain ZA [auth 4R] MOL2 format, chain AB [auth 4S] MOL2 format, chain BA [auth 4D] MOL2 format, chain CA [auth 4E] MOL2 format, chain FB [auth 4W] MOL2 format, chain HA [auth 4G] MOL2 format, chain JB [auth 4Z] MOL2 format, chain KA [auth 4L] MOL2 format, chain PA [auth 4Q] MOL2 format, chain QA [auth 4Q] MOL2 format, chain ZA [auth 4R] mmCIF format, chain AB [auth 4S] mmCIF format, chain BA [auth 4D] mmCIF format, chain CA [auth 4E] mmCIF format, chain FB [auth 4W] mmCIF format, chain HA [auth 4G] mmCIF format, chain JB [auth 4Z] mmCIF format, chain KA [auth 4L] mmCIF format, chain PA [auth 4Q] mmCIF format, chain QA [auth 4Q] mmCIF format, chain ZA [auth 4R]	AB [auth 4S] BA [auth 4D] CA [auth 4E] FB [auth 4W] HA [auth 4G] AB [auth 4S], BA [auth 4D], CA [auth 4E], FB [auth 4W], HA [auth 4G], JB [auth 4Z], KA [auth 4L], PA [auth 4Q], QA [auth 4Q], ZA [auth 4R]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AB [auth 4S] Focus chain BA [auth 4D] Focus chain CA [auth 4E] Focus chain FB [auth 4W] Focus chain HA [auth 4G] Focus chain JB [auth 4Z] Focus chain KA [auth 4L] Focus chain PA [auth 4Q] Focus chain QA [auth 4Q] Focus chain ZA [auth 4R] Interactions & Density Focus chain AB [auth 4S] Focus chain BA [auth 4D] Focus chain CA [auth 4E] Focus chain FB [auth 4W] Focus chain HA [auth 4G] Focus chain JB [auth 4Z] Focus chain KA [auth 4L] Focus chain PA [auth 4Q] Focus chain QA [auth 4Q] Focus chain ZA [auth 4R]
LPP (Subject of Investigation/LOI) Query on LPP Download Ideal Coordinates CCD File SDF format, chain AA [auth 4C] SDF format, chain IB [auth 4Z] MOL2 format, chain AA [auth 4C] MOL2 format, chain IB [auth 4Z] mmCIF format, chain AA [auth 4C] mmCIF format, chain IB [auth 4Z]	AA [auth 4C], IB [auth 4Z]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain AA [auth 4C] Focus chain IB [auth 4Z] Interactions & Density Focus chain AA [auth 4C] Focus chain IB [auth 4Z]
CUA (Subject of Investigation/LOI) Query on CUA Download Ideal Coordinates CCD File SDF format, chain NA [auth 4N] MOL2 format, chain NA [auth 4N] mmCIF format, chain NA [auth 4N]	NA [auth 4N]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain NA [auth 4N] Interactions & Density Focus chain NA [auth 4N]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain CB [auth 4T] SDF format, chain DB [auth 4T] SDF format, chain HB [auth 4X] MOL2 format, chain CB [auth 4T] MOL2 format, chain DB [auth 4T] MOL2 format, chain HB [auth 4X] mmCIF format, chain CB [auth 4T] mmCIF format, chain DB [auth 4T] mmCIF format, chain HB [auth 4X]	CB [auth 4T], DB [auth 4T], HB [auth 4X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CB [auth 4T] Focus chain DB [auth 4T] Focus chain HB [auth 4X] Interactions & Density Focus chain CB [auth 4T] Focus chain DB [auth 4T] Focus chain HB [auth 4X]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain UA [auth 4Q] MOL2 format, chain UA [auth 4Q] mmCIF format, chain UA [auth 4Q]	UA [auth 4Q]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain UA [auth 4Q] Interactions & Density Focus chain UA [auth 4Q]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain TA [auth 4Q] MOL2 format, chain TA [auth 4Q] mmCIF format, chain TA [auth 4Q]	TA [auth 4Q]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain TA [auth 4Q] Interactions & Density Focus chain TA [auth 4Q]
PER (Subject of Investigation/LOI) Query on PER Download Ideal Coordinates CCD File SDF format, chain YA [auth 4Q] MOL2 format, chain YA [auth 4Q] mmCIF format, chain YA [auth 4Q]	YA [auth 4Q]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain YA [auth 4Q] Interactions & Density Focus chain YA [auth 4Q]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain VA [auth 4Q] MOL2 format, chain VA [auth 4Q] mmCIF format, chain VA [auth 4Q]	VA [auth 4Q]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain VA [auth 4Q] Interactions & Density Focus chain VA [auth 4Q]