Mycobacterial supercomplex malate:quinone oxidoreductase assembly
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dm1
Q-score: 0.38
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung J, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein J
To Be Published
- Respiratory complex mqo:ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Heme c (618 Da, Ligand)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Probable malate:quinone oxidoreductase (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cardiolipin (1 kDa, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ovc
Q-score: 0.598
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ DOI: doi:10.1038/s41467-024-49628-9 Pubmed: 38902248 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
Structure of the human Fanconi anaemia Core complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7kzp
Q-score: 0.437
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core complex (1 MDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
Structure of the human Fanconi anaemia Core-ID complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7kzq
Q-score: 0.298
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core-id complex (1 MDa, Complex from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia, complementation group i (149 kDa, Protein from Homo sapiens)
Structure of the human Fanconi Anaemia Core-UBE2T-ID complex
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7kzr
Q-score: 0.298
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 t (22 kDa, Protein from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core-ube2t-id complex (1 MDa, Complex from Homo sapiens)
- Fanconi anemia, complementation group i (149 kDa, Protein from Homo sapiens)
Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in open state
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7kzs
Q-score: 0.303
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 t (22 kDa, Protein from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Dna (25-mer) (17 kDa, DNA from synthetic construct)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
- Dna (25-mer) (18 kDa, DNA from synthetic construct)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia, complementation group i (149 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core-ube2t-id-dna complex (1 MDa, Complex from Homo sapiens)
Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in intermediate state
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7kzt
Q-score: 0.297
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Dna (22-mer) (18 kDa, DNA from synthetic construct)
- Dna (22-mer) (17 kDa, DNA from synthetic construct)
- Ubiquitin-conjugating enzyme e2 t (22 kDa, Protein from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia, complementation group i (149 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core-ube2t-id-dna complex (1 MDa, Complex from Homo sapiens)
Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in closed state
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7kzv
Q-score: 0.293
Wang S, Wang R, Peralta C, Yaseen A, Pavletich NP
Nat Struct Mol Biol (2021) 28 pp. 300-309 [ DOI: doi:10.1038/s41594-021-00568-8 Pubmed: 33686268 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase fancl (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group c protein (66 kDa, Protein from Homo sapiens)
- Fanconi anemia group b protein (100 kDa, Protein from Homo sapiens)
- Fanconi anemia group e protein (61 kDa, Protein from Homo sapiens)
- Fanconi anemia group a protein (165 kDa, Protein from Homo sapiens)
- Fanconi anemia group f protein (45 kDa, Protein from Homo sapiens)
- Fanconi anemia group g protein (70 kDa, Protein from Homo sapiens)
- Dna (29-mer) (18 kDa, DNA from synthetic construct)
- Dna (29-mer) (17 kDa, DNA from synthetic construct)
- Ubiquitin-conjugating enzyme e2 t (22 kDa, Protein from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 100 (96 kDa, Protein from Homo sapiens)
- Fanconi anemia core complex-associated protein 20 (4 kDa, Protein from Homo sapiens)
- Fanconi anemia, complementation group i (149 kDa, Protein from Homo sapiens)
- Human fanconi anaemia core-ube2t-id-dna complex (1 MDa, Complex from Homo sapiens)
Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 6.5
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7bub
Q-score: 0.376
Zhang S, Loy T, Ng TS, Lim XN, Chew SV, Tan TY, Xu M, Kostyuchenko VA, Tukijan F, Shi J, Fink K, Lok SM
Cell Rep (2020) 31 pp. 107584-107584 [ DOI: doi:10.1016/j.celrep.2020.107584 Pubmed: 32348755 ]
- Dengue virus serotype2 e protein (54 kDa, Protein from Dengue virus 2)
- Sign-3c fab heavy chain (14 kDa, Protein from Homo sapiens)
- Complex of dengue virus serotype 2 with sign-3c fab (Complex from Homo sapiens)
- Dengue virus serotype 2 m protein (8 kDa, Protein from Dengue virus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sign-3c fab light chain (11 kDa, Protein from Homo sapiens)
- Dengue virus serotype 2 (Complex)
- Sign-3c fab (Complex from Dengue virus 2)
Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 8.0
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7bud
Q-score: 0.334
Zhang S, Loy T, Ng TS, Lim XN, Chew SV, Tan TY, Xu M, Kostyuchenko VA, Tukijan F, Shi J, Fink K, Lok SM
Cell Rep (2020) 31 pp. 107584-107584 [ DOI: doi:10.1016/j.celrep.2020.107584 Pubmed: 32348755 ]
- Sign-3c fab heavy chain (14 kDa, Protein from Homo sapiens)
- Complex of dengue virus serotype 2 with sign-3c fab (Complex from Homo sapiens)
- Dengue virus serotype 2 m protein (8 kDa, Protein from Dengue virus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sign-3c fab light chain (11 kDa, Protein from Homo sapiens)
- Dengue virus serotype 2 e protein (54 kDa, Protein from Dengue virus 2)
- Dengue virus serotype 2 (Complex)
- Sign-3c fab (Complex from Dengue virus 2)