Structure of human ceramide synthase 6 (CerS6) in complex with N-palmitoyl fumonisin B1
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8qz7
Q-score: 0.518
Pascoa TC, Pike ACW, Tautermann CS, Chi G, Traub M, Quigley A, Chalk R, Stefanic S, Thamm S, Pautsch A, Carpenter EP, Schnapp G, Sauer DB
Nat Struct Mol Biol (2024) [ Pubmed: 39528795 DOI: doi:10.1038/s41594-024-01414-3 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cers6-nb22 complex (114 kDa, Complex from Homo sapiens)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Isoform 2 of ceramide synthase 6 (42 kDa, Protein from Homo sapiens)
- Nanobody-22 (15 kDa, Protein from Vicugna pacos)
- (2~{r})-2-[2-[(5~{r},6~{r},7~{s},9~{s},11~{r},16~{r},18~{s},19~{s})-6-[(3~{r})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-19-(hexadecanoylamino)-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid (960 Da, Ligand)
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
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Probable malate:quinone oxidoreductase (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Heme c (618 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)
- 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 c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Palmitic acid (256 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme-a (852 Da, Ligand)
- Cytochrome aa3 subunit 2 (35 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 aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Respiratory complex mqo:ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Lpqe protein (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cardiolipin (1 kDa, Ligand)
Resolution: 3.61 Å
EM Method: Helical reconstruction
Fitted PDBs: 8qbd
Q-score: 0.428
Kefauver JM, Hakala M, Zou L, Alba J, Espadas J, Tettamanti MG, Gajic J, Gabus C, Campomanes P, Estrozi LF, Sen NE, Vanni S, Roux A, Desfosses A, Loewith R
Nature (2024) 632 pp. 664-671 [ DOI: doi:10.1038/s41586-024-07720-6 Pubmed: 39048819 ]
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Helical assembly of recombinant pil1 protein tubulating +pip2/+sterol lipid mixture (dopc, dope, dops, cholesterol, pi(4,5)p2 35:20:20:15:10) (Complex from Saccharomyces cerevisiae)
- D-myo-inositol-1,4,5-triphosphate (420 Da, Ligand)
- Sphingolipid long chain base-responsive protein pil1 (38 kDa, Protein from Saccharomyces cerevisiae)
ST171-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8pjk
Q-score: 0.611
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- St171-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- 6-[3-[2-(2-methoxyphenoxy)ethylamino]propoxy]-4~{h}-1,4-benzoxazin-3-one (372 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pkm
Q-score: 0.468
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- Befiradol-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- (3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone (393 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
Cannabinoid receptor 1-Gi complex with novel ligand
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8gag
Q-score: 0.463
Tummino TA, Iliopoulos-Tsoutsouvas C, Braz JM, O'Brien ES, Krishna Kumar K, Makriyannis M, Basbaum AI, Shoichet BK
To Be Published
- Scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cannabinoid receptor 1 (55 kDa, Protein from Homo sapiens)
- Methyl (2r)-2-({(1m)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1h-pyrazole-3-carbonyl}amino)-2-(thiophen-2-yl)propanoate (437 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Signaling complex of the cannabinoid receptor 1 bound to gi (Complex from Homo sapiens)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8dty
Q-score: 0.309
Hu Y, Iyer KA, Nayak AR, Eltit JM, Kurebayashi N, Murayama T, Samso M
To Be Published
- Recombinant mouse ryr2 triple phosphomimetic mutant s2807d/s2813d/s2030d in complex with fkbp12.6 and nanodisc under closed-state conditions (2 MDa, Complex from Mus musculus)
- Ryanodine receptor 2 (565 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8dtz
Q-score: 0.302
Hu Y, Iyer KA, Nayak AR, Eltit JM, Kurebayashi N, Murayama T, Samso M
To Be Published
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Recombinant mouse ryr2 triple phosphonull mutant s2807a/s2813a/s2030a in complex with fkbp12.6 and nanodisc under closed-state conditions (2 MDa, Complex from Mus musculus)
- Ryanodine receptor 2 (565 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8dvv
Q-score: 0.318
Hu Y, Iyer KA, Nayak AR, Eltit JM, Kurebayashi N, Murayama T, Samso M
To Be Published
- Ryanodine receptor 2 (565 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Recombinant mouse ryr2 triple phosphomimetic mutant s2807d/s2813d/s2030d in complex with fkbp12.6 and nanodisc under open-state conditions (2 MDa, Complex from Mus musculus)
cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8smr
Q-score: 0.608
Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Adelroth P, Vahidi S, Howell PL, Rubinstein JL
PNAS (2023) 120 pp. e2307093120-e2307093120 [ DOI: doi:10.1073/pnas.2307093120 Pubmed: 37751552 ]
- Calcium ion (40 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit (34 kDa, Protein from Pseudomonas aeruginosa)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c5 (13 kDa, Protein from Pseudomonas aeruginosa)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit ii (22 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome b (46 kDa, Protein from Pseudomonas aeruginosa)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome c4 (18 kDa, Protein from Pseudomonas aeruginosa)
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome-c oxidase (52 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome bc1-cbb3 supercomplex (374 MDa, Complex from Pseudomonas aeruginosa)
- (2r)-2-(methoxymethyl)-4-{[(25r)-spirost-5-en-3beta-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-beta-d-glucopyranoside (855 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome c1 (26 kDa, Protein from Pseudomonas aeruginosa)