Cryo-EM structure of the yeast SPT-Orm2-Dimer complex, local refinement of a monomer
Korner C, Schafer JH, Esch BM, Parey K, Walter S, Teis D, Januliene D, Schmidt O, Moeller A, Frohlich F
Cell Rep (2024) 43 pp. 114627-114627 [ Pubmed: 39167489 DOI: doi:10.1016/j.celrep.2024.114627 ]
- Complex of lcb1, lcb2, orm2 and tsc3 (160 kDa, Complex from Saccharomyces cerevisiae)
The ABCB1 L335C mutant (mABCB1) in the Apo state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8avy
Q-score: 0.54
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q
eLife (2024) 12 [ Pubmed: 38259172 DOI: doi:10.7554/eLife.90174 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Atp-dependent translocase abcb1 (146 kDa, Protein from Mus musculus)
- Abcb1 (140 MDa, Complex from Mus musculus)
The ABCB1 L335C mutant (mABCB1) in the outward facing state
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7zk4
Q-score: 0.569
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q
eLife (2024) 12 [ Pubmed: 38259172 DOI: doi:10.7554/eLife.90174 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Atp-dependent translocase abcb1 (146 kDa, Protein from Mus musculus)
- Abcb1 (140 MDa, Complex from Mus musculus)
ABCB1 L335C mutant (mABCB1) in the outward facing state bound to AAC
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7zk5
Q-score: 0.571
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q
eLife (2024) 12 [ Pubmed: 38259172 DOI: doi:10.7554/eLife.90174 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Atp-dependent translocase abcb1 (146 kDa, Protein from Mus musculus)
- (4~{s},11~{s},18~{s})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione (494 Da, Ligand)
- Abcb1 (140 MDa, Complex from Mus musculus)
ABCB1 V978C mutant (mABCB1) in the outward facing state bound to AAC
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7zka
Q-score: 0.533
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q
eLife (2024) 12 [ Pubmed: 38259172 DOI: doi:10.7554/eLife.90174 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp-dependent translocase abcb1 (146 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- (4~{s},11~{s},18~{s})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione (494 Da, Ligand)
- Abcb1 (140 MDa, Complex from Mus musculus)
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7ph3
Q-score: 0.555
Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA
Sci Adv (2022) 8 pp. eabn6845-eabn6845 [ Pubmed: 36223470 DOI: doi:10.1126/sciadv.abn6845 ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Atp-dependent lipid a-core flippase (65 kDa, Protein from Escherichia coli K-12)
- (1~{r},4~{r},11~{s},14~{s},19~{z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione (524 Da, Ligand)
- Water (18 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- E. coli msba in complex with nanobody nb_msba#1, labeled with gd-dota at cys60 (Complex from Escherichia coli)
- Gadolinium atom (157 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Nanobody nb_msba#1 (12 kDa, Protein from Vicugna pacos)
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7ph4
Q-score: 0.569
Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA
Sci Adv (2022) 8 pp. eabn6845-eabn6845 [ Pubmed: 36223470 DOI: doi:10.1126/sciadv.abn6845 ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- (1~{r},4~{r},11~{s},14~{s},19~{z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione (524 Da, Ligand)
- Nanobody nb_msba#1 (12 kDa, Protein from Vicugna pacos)
- Water (18 Da, Ligand)
- Atp-dependent lipid a-core flippase (65 kDa, Protein from Escherichia coli (strain K12))
- Gadolinium atom (157 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Amp-pnp bound e. coli msba in complex with nanobody nb_msba#1, labeled with gd-dota at t68c (Complex)
Cryo-EM structure of a respiratory complex I
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7o71
Q-score: 0.644
Parey K, Lasham J, Mills DJ, Djurabekova A, Haapanen O, Yoga EG, Xie H, Kuhlbrandt W, Sharma V, Vonck J, Zickermann V
Sci Adv (2021) 7 pp. eabj3221-eabj3221 [ Pubmed: 34767441 DOI: doi:10.1126/sciadv.abj3221 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Nadh-ubiquinone oxidoreductase 78 kda subunit (79 kDa, Protein from Candida lipolytica)
- Cardiolipin (1 kDa, Ligand)
- Nadh-ubiquinone oxidoreductase chain 4 (54 kDa, Protein from Yarrowia lipolytica)
- Mitochondrial nadh:ubiquinone oxidoreductase (1 MDa, Complex from Yarrowia lipolytica)
- Subunit nujm of nadh:ubiquinone oxidoreductase (complex i) (20 kDa, Protein from Yarrowia lipolytica)
- Subunit nuvm of nadh:ubiquinone oxidoreductase (complex i) (7 kDa, Protein from Yarrowia lipolytica)
- Nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (53 kDa, Protein from Candida lipolytica)
- Subunit ni8m of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Candida lipolytica)
- Subunit nuxm of nadh:ubiquinone oxidoreductase (complex i) (18 kDa, Protein from Candida lipolytica)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Subunit nesm of nadh:ubiquinone oxidoreductase (complex i) (28 kDa, Protein from Yarrowia lipolytica)
- Flavin mononucleotide (456 Da, Ligand)
- Subunit ni2m of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Candida lipolytica)
- Nadh dehydrogenase subunit 2 (53 kDa, Protein from Yarrowia lipolytica)
- Nadh-ubiquinone oxidoreductase chain 5 (73 kDa, Protein from Yarrowia lipolytica)
- Subunit niam of nadh:ubiquinone oxidoreductase (complex i) (17 kDa, Protein from Yarrowia lipolytica)
- Nadh-ubiquinone oxidoreductase chain 6 (20 kDa, Protein from Candida lipolytica)
- Nadh-ubiquinone oxidoreductase 40 kda subunit (42 kDa, Protein from Candida lipolytica)
- Subunit nupm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Nadh-ubiquinone oxidoreductase chain 1 (38 kDa, Protein from Yarrowia lipolytica)
- Subunit nufm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nunm of nadh:ubiquinone oxidoreductase (complex i) (13 kDa, Protein from Candida lipolytica)
- 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (758 Da, Ligand)
- Subunit nb8m of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Candida lipolytica)
- Acyl carrier protein acpm1 of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Candida lipolytica)
- Subunit nb4m of protein nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
- Subunit nuym of nadh:ubiquinone oxidoreductase (complex i) (18 kDa, Protein from Candida lipolytica)
- Nadh-ubiquinone oxidoreductase chain 4l (9 kDa, Protein from Yarrowia lipolytica)
- Subunit nuim of nadh:ubiquinone oxidoreductase (complex i) (25 kDa, Protein from Candida lipolytica)
- Subunit nb6m of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
- Subunit n7bm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nidm of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Candida lipolytica)
- Subunit nukm of nadh:ubiquinone oxidoreductase (complex i) (23 kDa, Protein from Candida lipolytica)
- Subunit nipm of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Candida lipolytica)
- Phosphatidylinositol (887 Da, Ligand)
- Subunit ni9m of protein nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Subunit numm of protein nadh:ubiquinone oxidoreductase (complex i) (15 kDa, Protein from Candida lipolytica)
- Subunit nb5m of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Candida lipolytica)
- Zinc ion (65 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Subunit nugm of nadh:ubiquinone oxidoreductase (complex i) (32 kDa, Protein from Candida lipolytica)
- Subunit nebm of nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Subunit nuum of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Diundecyl phosphatidyl choline (622 Da, Ligand)
- Subunit nb2m of nadh:ubiquinone oxidoreductase (complex i) (6 kDa, Protein from Yarrowia lipolytica)
- Water (18 Da, Ligand)
- Nucm protein (52 kDa, Protein from Yarrowia lipolytica)
- Subunit nuzm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- Acyl carrier protein acpm2 of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Candida lipolytica)
- Nadh-ubiquinone oxidoreductase chain 3 (14 kDa, Protein from Yarrowia lipolytica)
- Subunit nuhm of nadh:ubiquinone oxidoreductase (complex i) (27 kDa, Protein from Candida lipolytica)
- Iron/sulfur cluster (351 Da, Ligand)
- Subunit nimm of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Candida lipolytica)
- S-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate (568 Da, Ligand)
Cryo-EM structure of a respiratory complex I F89A mutant
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 6y79
Q-score: 0.505
Galemou Yoga E, Parey K, Djurabekova A, Haapanen O, Siegmund K, Zwicker K, Sharma V, Zickermann V, Angerer H
Nat Commun (2020) 11 pp. 6008-6008 [ Pubmed: 33243981 DOI: doi:10.1038/s41467-020-19778-7 ]
- Subunit nuam of nadh:ubiquinone oxidoreductase (complex i) (79 kDa, Protein from Yarrowia lipolytica)
- Subunit nucm of nadh:ubiquinone oxidoreductase (complex i) (52 kDa, Protein from Yarrowia lipolytica)
- Subunit nipm of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Yarrowia lipolytica)
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Subunit nukm of nadh:ubiquinone oxidoreductase (complex i) (23 kDa, Protein from Yarrowia lipolytica)
- Subunit ni8m of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Mitochondrial nadh:ubiquinone oxidoreductase (1 MDa, Complex from Yarrowia lipolytica)
- Subunit nujm of nadh:ubiquinone oxidoreductase (complex i) (20 kDa, Protein from Yarrowia lipolytica)
- Subunit nuvm of nadh:ubiquinone oxidoreductase (complex i) (7 kDa, Protein from Yarrowia lipolytica)
- Acyl carrier protein acpm1 of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Yarrowia lipolytica)
- Subunit nugm of nadh:ubiquinone oxidoreductase (complex i) (32 kDa, Protein from Yarrowia lipolytica)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Subunit nu1m of nadh:ubiquinone oxidoreductase (complex i) (38 kDa, Protein from Yarrowia lipolytica)
- Subunit nesm of nadh:ubiquinone oxidoreductase (complex i) (28 kDa, Protein from Yarrowia lipolytica)
- Flavin mononucleotide (456 Da, Ligand)
- Subunit niam of nadh:ubiquinone oxidoreductase (complex i) (17 kDa, Protein from Yarrowia lipolytica)
- Subunit nupm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Acyl carrier protein acpm2 of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Yarrowia lipolytica)
- Subunit nufm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nuem of nadh:ubiquinone oxidoreductase (complex i) (42 kDa, Protein from Yarrowia lipolytica)
- Ubiquinone-9 (795 Da, Ligand)
- Subunit numm of protein nadh:ubiquinone oxidoreductase (complex i) (15 kDa, Protein from Yarrowia lipolytica)
- Subunit nb8m of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Yarrowia lipolytica)
- Subunit nb5m of nadh:ubiquinone oxidoreductase (complex i) (10 kDa, Protein from Yarrowia lipolytica)
- Subunit nuhm of nadh:ubiquinone oxidoreductase (complex i) (27 kDa, Protein from Yarrowia lipolytica)
- Subunit nimm of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Subunit n7bm of nadh:ubiquinone oxidoreductase (complex i) (16 kDa, Protein from Yarrowia lipolytica)
- Subunit nuxm of nadh:ubiquinone oxidoreductase (complex i) (18 kDa, Protein from Yarrowia lipolytica)
- Subunit ni2m of nadh:ubiquinone oxidoreductase (complex i) (12 kDa, Protein from Yarrowia lipolytica)
- Subunit nunm of nadh:ubiquinone oxidoreductase (complex i) (13 kDa, Protein from Yarrowia lipolytica)
- Subunit nulm of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Subunit nu6m of nadh:ubiquinone oxidoreductase (complex i) (20 kDa, Protein from Yarrowia lipolytica)
- Subunit nuim of nadh:ubiquinone oxidoreductase (complex i) (25 kDa, Protein from Yarrowia lipolytica)
- Subunit ni9m of nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Phosphatidylinositol (887 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Subunit nubm of nadh:ubiquinone oxidoreductase (complex i) (53 kDa, Protein from Yarrowia lipolytica)
- Subunit nidm of nadh:ubiquinone oxidoreductase (complex i) (11 kDa, Protein from Yarrowia lipolytica)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Subunit nu5m of nadh:ubiquinone oxidoreductase (complex i) (73 kDa, Protein from Yarrowia lipolytica)
- Subunit nb4m of protein nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Yarrowia lipolytica)
- Subunit nuym of nadh:ubiquinone oxidoreductase (complex i) (18 kDa, Protein from Yarrowia lipolytica)
- Subunit nebm of nadh:ubiquinone oxidoreductase (complex i) (8 kDa, Protein from Yarrowia lipolytica)
- Subunit nuum of nadh:ubiquinone oxidoreductase (complex i) (9 kDa, Protein from Yarrowia lipolytica)
- Diundecyl phosphatidyl choline (622 Da, Ligand)
- Subunit nb2m of nadh:ubiquinone oxidoreductase (complex i) (6 kDa, Protein from Yarrowia lipolytica)
- Subunit nb6m of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Yarrowia lipolytica)
- Subunit nu2m of nadh:ubiquinone oxidoreductase (complex i) (53 kDa, Protein from Yarrowia lipolytica)
- Subunit nuzm of nadh:ubiquinone oxidoreductase (complex i) (19 kDa, Protein from Yarrowia lipolytica)
- Subunit nu4m of nadh:ubiquinone oxidoreductase (complex i) (54 kDa, Protein from Yarrowia lipolytica)
- (7r,17e,20e)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosa-17,20-dien-1-aminium 4-oxide (759 Da, Ligand)
- Subunit nu3m of nadh:ubiquinone oxidoreductase (complex i) (14 kDa, Protein from Yarrowia lipolytica)
- Iron/sulfur cluster (351 Da, Ligand)
- S-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate (568 Da, Ligand)