Structure of the II2-III2-IV2 mitochondrial supercomplex from the parasite Perkinsus marinus
Wu, F., Muhleip, A., Gruhl, T., Sheiner, L., Marechal, A., Amunts, A.(2024) bioRxiv 
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
(2024) bioRxiv 
Macromolecule Content 
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5K7H0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KED7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L7H1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LUF4 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Merozoite surface protein, putative | E [auth 4E] | 152 | Perkinsus marinus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L0U1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin, putative | F [auth 4F] | 80 | Perkinsus marinus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KBY9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KJE7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L104 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LPW2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L533 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KST9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KPD1 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LDS7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5K5E4 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LG07 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LK31 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F8SRI9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5KSX3 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L3V7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase 13 | T [auth 4T] | 121 | Perkinsus marinus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5K4P8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LG64 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 22 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cg8 protein | V [auth 4V] | 185 | Perkinsus marinus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LR54 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5L0W2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 24 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome Coxidase subunit, putative | X [auth 4X] | 226 | Perkinsus marinus | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LUB2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LUI5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C5LYX8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
| Ligands 11 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CDL (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | BB [auth 4S] DA [auth 4E] EA [auth 4E] EB [auth 4U] GA [auth 4F] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L | |||
| HEA (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | WA [auth 4Q], XA [auth 4Q] | HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L | |||
| PC1 (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | FA [auth 4F] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N | |||
| PEE (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AB [auth 4S] BA [auth 4D] CA [auth 4E] FB [auth 4W] HA [auth 4G] | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N | |||
| LPP (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | AA [auth 4C], IB [auth 4Z] | 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C35 H69 O8 P PORPENFLTBBHSG-MGBGTMOVSA-N | |||
| CUA (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | NA [auth 4N] | DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N | |||
| ZN (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | CB [auth 4T], DB [auth 4T], HB [auth 4X] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| CU (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | UA [auth 4Q] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
| K (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | TA [auth 4Q] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
| PER (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | YA [auth 4Q] | PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N | |||
| MG (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | VA [auth 4Q] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
| Funding Organization | Location | Grant Number |
|---|---|---|
| European Research Council (ERC) | European Union | ERC-2018-StG-805230 |