Differential substrate utilization by yeast respiratory supercomplexes
Eldeeb, M.H., Cosner, Z., Mays, J., Carlstrom, A., Rodriguez, G., Berndtsson, J., Ott, M., Fontanesi, F.To be published.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 1, mitochondrial | A, V [auth K] | 457 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07256  Go to UniProtKB:  P07256 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07256 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B, W [auth L] | 368 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07257  Go to UniProtKB:  P07257 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07257 | ||||
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Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b | C, X [auth M] | 385 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.8 | ![]() |
UniProt | |||||
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00163  Go to UniProtKB:  P00163 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00163 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c1, heme protein, mitochondrial | D, Y [auth N] | 309 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.8 | ![]() |
UniProt | |||||
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07143  Go to UniProtKB:  P07143 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07143 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E, Z [auth O] | 215 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.8 | ![]() |
UniProt | |||||
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08067  Go to UniProtKB:  P08067 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08067 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 6, mitochondrial | AA [auth P], F | 147 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00127  Go to UniProtKB:  P00127 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00127 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial | BA [auth Q], G | 183 | Saccharomyces cerevisiae W303 | Mutation(s): 0  Gene Names: QCR7, CRO1, UCR7, YDR529C, D9719.32, COX8, YLR395C, L8084.14 | ![]() |
UniProt | |||||
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00128  Go to UniProtKB:  P00128 | |||||
Find proteins for P04039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04039  Go to UniProtKB:  P04039 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | P00128P04039 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 8, mitochondrial | CA [auth R], H | 94 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08525  Go to UniProtKB:  P08525 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08525 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 9, mitochondrial | DA [auth S], I | 66 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22289  Go to UniProtKB:  P22289 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22289 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome b-c1 complex subunit 10, mitochondrial | EA [auth T], J | 77 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P37299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P37299  Go to UniProtKB:  P37299 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P37299 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 1 | FA [auth m], K [auth a] | 534 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00401  Go to UniProtKB:  P00401 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00401 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 2 | GA [auth n], L [auth b] | 251 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Find proteins for P00410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00410  Go to UniProtKB:  P00410 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00410 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 3 | HA [auth o], M [auth c] | 269 | Saccharomyces cerevisiae W303 | Mutation(s): 0  EC: 7.1.1.9 | ![]() |
UniProt | |||||
Find proteins for P00420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00420  Go to UniProtKB:  P00420 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00420 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 4, mitochondrial | IA [auth p], N [auth d] | 155 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04037  Go to UniProtKB:  P04037 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04037 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 5A, mitochondrial | JA [auth q], O [auth e] | 153 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P00424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00424  Go to UniProtKB:  P00424 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00424 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 6, mitochondrial | KA [auth r], P [auth f] | 148 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00427  Go to UniProtKB:  P00427 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00427 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 7, mitochondrial | LA [auth s], Q [auth g] | 60 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10174  Go to UniProtKB:  P10174 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P10174 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 9, mitochondrial | MA [auth u], R [auth i] | 59 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07255  Go to UniProtKB:  P07255 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07255 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 12, mitochondrial | NA [auth v], S [auth j] | 83 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for Q01519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01519  Go to UniProtKB:  Q01519 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q01519 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 13, mitochondrial | OA [auth w], T [auth k] | 129 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for P32799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32799  Go to UniProtKB:  P32799 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P32799 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c oxidase subunit 26, mitochondrial | PA [auth x], U [auth l] | 66 | Saccharomyces cerevisiae W303 | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q2V2P9  Go to UniProtKB:  Q2V2P9 | |||||
Entity Groups   | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2V2P9 | ||||
Sequence AnnotationsExpand | |||||
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| Ligands 19 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CDL Query on CDL | BB [auth D] DB [auth E] EB [auth H] IC [auth N] KC [auth O] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L | |||
| HEA Query on HEA | JB [auth a], LB [auth a], QC [auth m], SC [auth m] | HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L | |||
| CN3 Query on CN3 | OB [auth a], VC [auth m] | (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate C36 H68 O17 P2 FMNZIMGRZPIVKW-XWHIBYANSA-N | |||
| PTY Query on PTY | AD [auth n] BD [auth o] GB [auth I] MB [auth a] NC [auth S] | PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N | |||
| PCF Query on PCF | DD [auth w] ED [auth x] FB [auth H] HB [auth I] MC [auth R] | 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE C40 H80 N O8 P KILNVBDSWZSGLL-KXQOOQHDSA-N | |||
| 8PE Query on 8PE | AC [auth M], SA [auth C] | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C37 H74 N O8 P RFJQNULIDFTTLL-PGUFJCEWSA-N | |||
| PEF Query on PEF | GC [auth N] IB [auth J] PB [auth a] PC [auth T] WC [auth m] | DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C37 H74 N O8 P SLKDGVPOSSLUAI-PGUFJCEWSA-N | |||
| CN5 Query on CN5 | TA [auth C] | (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate C26 H52 O13 P2 UKWPDXFRXMWSMQ-VWLOTQADSA-N | |||
| HEC Query on HEC | AB [auth D], HC [auth N] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N | |||
| HEM Query on HEM | CC [auth M], EC [auth M], VA [auth C], XA [auth C] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
| 9PE Query on 9PE | DC [auth M], WA [auth C] | (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate C30 H60 N O8 P RWBMCOYSJCETON-MUUNZHRXSA-N | |||
| UQ6 Query on UQ6 | BC [auth M], FC [auth M], UA [auth C], YA [auth C] | 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL C39 H60 O4 DYOSCPIQEYRQEO-XQCASOQKSA-N | |||
| 6PH Query on 6PH | RA [auth C], ZB [auth M] | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate C31 H61 O8 P UOOPRMYYAWVCCZ-GDLZYMKVSA-N | |||
| FES Query on FES | CB [auth E], JC [auth O] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N | |||
| CUA Query on CUA | SB [auth b], ZC [auth n] | DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N | |||
| ZN Query on ZN | CD [auth p], VB [auth d] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| CU Query on CU | KB [auth a], RC [auth m] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
| CA Query on CA | NB [auth a], UC [auth m] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
| MG Query on MG | QB [auth b], XC [auth n] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | Coot | 0.9.8.7 |
| RECONSTRUCTION | cryoSPARC | 4.2 |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Defense (DOD, United States) | United States | W911NF-21-1-0359 |