Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration
Yaikhomba, M., Hirst, J., Croll, T.I., Spikes, T.E.To be published.
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit A | 121 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B498 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit B | 175 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B497 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit C | 208 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B496 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit D | 412 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B495 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH dehydrogenase subunit E | 239 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B494 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit F | 431 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B491 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase | 674 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B489 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit H | 345 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B487 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit I | 163 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B486 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit J | 199 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B483 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit K | 101 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B482 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH dehydrogenase subunit L | 703 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B481 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH dehydrogenase subunit M | 513 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B480 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH-quinone oxidoreductase subunit N | 499 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | ![]() | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B479 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAD-dependent epimerase/dehydratase | O [auth P] | 330 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1AZB0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ETC complex I subunit conserved region | P [auth Q] | 103 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B1M0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Zinc finger CHCC-type domain-containing protein | Q [auth R] | 62 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B357 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protein-L-isoaspartate O-methyltransferase | R [auth Z] | 217 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B5L6 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b | S [auth a], V [auth d] | 440 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B4F3 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c1 | T [auth b], W [auth e] | 450 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B4F4 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquinol-cytochrome c reductase iron-sulfur subunit | U [auth c], X [auth f] | 195 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1.8 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B4F2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 22 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 1 | CA [auth k], Y [auth g] | 558 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B3D7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 23 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 2 | DA [auth l], Z [auth h] | 298 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1BA41 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 24 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| cytochrome-c oxidase | AA [auth i], EA [auth m] | 274 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1BA37 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 25 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Aa3 type cytochrome c oxidase subunit IV | BA [auth j], FA [auth n] | 66 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1AZ52 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 26 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c, class I | GA [auth o], HA [auth p] | 176 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B311 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 27 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH:ubiquinone oxidoreductase 17.2 kD subunit | IA [auth q] | 124 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B1H8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 28 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Transmembrane helix of unknown identity | JA [auth r] | 35 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
Entity ID: 29 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Transmembrane helix of unknown identity | KA [auth s] | 30 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
Entity ID: 30 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| cytochrome-c oxidase | LA [auth t] | 539 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B351 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 31 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase, cbb3-type, subunit II | MA [auth u] | 241 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B350 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 32 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cbb3-type cytochrome c oxidase subunit CcoP | NA [auth v] | 349 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B348 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
| Ligands 15 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CDL Download:Ideal Coordinates CCD File | CB [auth a] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L | |||
| U10 Download:Ideal Coordinates CCD File | DB [auth a], FB [auth a], KB [auth d], NB [auth d], XA [auth H] | UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N | |||
| HEA (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | TB [auth g], UB [auth g], YB [auth k], ZB [auth k] | HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L | |||
| HEC (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | IB [auth b], IC [auth u], JC [auth v], KC [auth v], PB [auth e] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N | |||
| HEM (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | EB [auth a] EC [auth t] FC [auth t] GB [auth a] LB [auth d] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
| DU0 Download:Ideal Coordinates CCD File | AB [auth N], QB [auth f], WA [auth H] | 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol C32 H52 O5 GFDJQXOBWHMOSQ-LEZUHYJESA-N | |||
| FMN (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | SA [auth F] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N | |||
| SF4 Download:Ideal Coordinates CCD File | OA [auth B] RA [auth F] TA [auth G] UA [auth G] YA [auth I] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
| FES Download:Ideal Coordinates CCD File | JB [auth c], QA [auth E], RB [auth f], VA [auth G] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N | |||
| CUA Download:Ideal Coordinates CCD File | CC [auth l], XB [auth h] | DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N | |||
| ZN Download:Ideal Coordinates CCD File | BB [auth R] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| CU Download:Ideal Coordinates CCD File | AC [auth k], DC [auth t], VB [auth g] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
| MN Download:Ideal Coordinates CCD File | WB [auth g] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N | |||
| CA Download:Ideal Coordinates CCD File | BC [auth k] GC [auth t] HB [auth b] HC [auth t] OB [auth e] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
| NA Download:Ideal Coordinates CCD File | PA [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N | |||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| FME Query on FME | A | L-PEPTIDE LINKING | C6 H11 N O3 S | MET | |
| 2MR Query on 2MR | D | L-PEPTIDE LINKING | C8 H18 N4 O2 | ARG | |
| UNK Query on UNK | JA [auth r] | L-PEPTIDE LINKING | C4 H9 N O2 | -- | |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Medical Research Council (MRC, United Kingdom) | United Kingdom | MC_UU_00015/2 and MC_UU_00028/1 |