Complex III2 from Yarrowia lipolytica, combined datasets, consensus refinement
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8ab6
Q-score: 0.757
IUCrJ (2023) 10 pp. 27-37 [ DOI: doi:10.1107/S2052252522010570 Pubmed: 36598500 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Water (18 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Complex iii2, consensus refinement of combined datasets (Cellular component from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
Complex III2 from Yarrowia lipolytica, atovaquone and antimycin A bound
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ab7
Q-score: 0.525
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione (366 Da, Ligand)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- [(2r,3s,6s,7r,8r)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate (548 Da, Ligand)
- Heme c (618 Da, Ligand)
- Complex iii2, atovaquone and antimycin a bound (Cellular component from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2, b-position, with decylubiquinone and ascorbate-reduced
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8ab8
Q-score: 0.625
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Complex iii2, b-position, with decylubiquinone and ascorbate-reduced (Cellular component from Yarrowia lipolytica)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione (322 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, b-position
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ab9
Q-score: 0.524
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Complex iii2, ascorbate-reduced, b-position (Cellular component from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, int-position
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8aba
Q-score: 0.537
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Complex iii2, ascorbate-reduced, int-position (Cellular component from Yarrowia lipolytica)
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (7 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, ascorbate-reduced, c-position
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8abb
Q-score: 0.54
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Complex iii2, ascorbate-reduced, c-position (Cellular component from Yarrowia lipolytica)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, b-position
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8abe
Q-score: 0.656
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Complex iii2, oxidised with ferricyanide, b-position (Cellular component from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, int-position
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8abf
Q-score: 0.652
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Complex iii2, oxidised with ferricyanide, int-position (Cellular component from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, c-position
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8abg
Q-score: 0.654
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Complex iii2, oxidised with ferricyanide, c-position (Cellular component from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Complex III2 from Yarrowia lipolytica, antimycin A bound, b-position
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8abh
Q-score: 0.49
IUCrJ (2023) 10 pp. 27-37 [ Pubmed: 36598500 DOI: doi:10.1107/S2052252522010570 ]
- Yali0a14806p (52 kDa, Protein from Yarrowia lipolytica)
- Yali0f24673p (15 kDa, Protein from Yarrowia lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome b-c1 complex subunit 2, mitochondrial (44 kDa, Protein from Yarrowia lipolytica)
- Yali0a17468p (36 kDa, Protein from Yarrowia lipolytica)
- 1,2-dimyristoyl-sn-glycero-3-phosphate (591 Da, Ligand)
- Complex iii2, with antimycin a, b-position (Cellular component from Yarrowia lipolytica)
- Cytochrome b (43 kDa, Protein from Yarrowia lipolytica)
- [(2r,3s,6s,7r,8r)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate (548 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Yarrowia lipolytica)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Yarrowia lipolytica)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome b-c1 complex subunit 7 (14 kDa, Protein from Yarrowia lipolytica)
- Complex iii subunit 9 (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Yali0c12210p (9 kDa, Protein from Yarrowia lipolytica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)