Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8jru
Q-score: 0.438
Chen K, Zhang C, Lin S, Yan X, Cai H, Yi C, Ma L, Chu X, Liu Y, Zhu Y, Han S, Zhao Q, Wu B
Nature (2023) 620 pp. 904-910 [ Pubmed: 37558880 DOI: doi:10.1038/s41586-023-06420-x ]
- The glucagon receptor bound to beta-arrestin 1 (Complex from Homo sapiens)
- Ha signal peptide,hpc4 purification tag,glucagon receptor,c-terminal tail of vasopressin v2 receptor (54 kDa, Protein from Homo sapiens)
- Nanobody 32 (13 kDa, Protein from Escherichia phage EcSzw-2)
- Beta-arrestin 1 and single-chain fragment variable 30 (scfv30) (69 kDa, Protein from Bos taurus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8jrv
Q-score: 0.431
Chen K, Zhang C, Lin S, Yan X, Cai H, Yi C, Ma L, Chu X, Liu Y, Zhu Y, Han S, Zhao Q, Wu B
Nature (2023) 620 pp. 904-910 [ Pubmed: 37558880 DOI: doi:10.1038/s41586-023-06420-x ]
- The glucagon receptor bound to glucagon and beta-arrestin 1 (Complex from Homo sapiens)
- Glucagon (3 kDa, Protein from Homo sapiens)
- Nanobody 32 (13 kDa, Protein from Escherichia phage EcSzw-2)
- Beta-arrestin 1 and single-chain fragment variable 30 (scfv30) (69 kDa, Protein from Homo sapiens)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Ha signal peptide,hpc4 purification tag,glucagon receptor,c-terminal tail of vasopressin v2 receptor (54 kDa, Protein from Homo sapiens)
Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 7w9k
Q-score: 0.507
Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N
Cell Rep (2022) 39 pp. 110735-110735 [ Pubmed: 35476982 DOI: doi:10.1016/j.celrep.2022.110735 ]
- Water (18 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 in complex with auxiliary beta subunits (279 MDa, Complex from Homo sapiens)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- (2s,3r,4e)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (421 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of human Nav1.7(E406K)-beta1-beta2 complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7w9l
Q-score: 0.414
Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N
Cell Rep (2022) 39 pp. 110735-110735 [ Pubmed: 35476982 DOI: doi:10.1016/j.celrep.2022.110735 ]
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 in complex with auxiliary beta subunits (279 MDa, Complex from Homo sapiens)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7w9m
Q-score: 0.437
Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N
Cell Rep (2022) 39 pp. 110735-110735 [ Pubmed: 35476982 DOI: doi:10.1016/j.celrep.2022.110735 ]
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- (1r,5r,6r,7r,9s,11s,12s,13s,14s)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) (319 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 in complex with auxiliary beta subunits (279 MDa, Complex from Homo sapiens)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7w9p
Q-score: 0.456
Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N
Cell Rep (2022) 39 pp. 110735-110735 [ Pubmed: 35476982 DOI: doi:10.1016/j.celrep.2022.110735 ]
- [(3as,4r,10as)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3h,8h-pyrrolo[1,2-c]purin-4-yl]methyl carbamate (299 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 in complex with auxiliary beta subunits (279 MDa, Complex from Homo sapiens)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- (2s,3r,4e)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (421 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7w9t
Q-score: 0.431
Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N
Cell Rep (2022) 39 pp. 110735-110735 [ Pubmed: 35476982 DOI: doi:10.1016/j.celrep.2022.110735 ]
- [(3as,4r,10as)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3h,8h-pyrrolo[1,2-c]purin-4-yl]methyl carbamate (299 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- Human nav1.7 in complex with beta1, beta2 and huwentoxin (Complex from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the PGE2-bound EP2-Gs complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7cx2
Q-score: 0.536
Qu C, Mao C, Xiao P, Shen Q, Zhong YN, Yang F, Shen DD, Tao X, Zhang H, Yan X, Zhao RJ, He J, Guan Y, Zhang C, Hou G, Zhang PJ, Hou G, Li Z, Yu X, Chai RJ, Guan YF, Sun JP, Zhang Y
Sci Adv (2021) 7 [ Pubmed: 33811074 DOI: doi:10.1126/sciadv.abf1268 ]
- Water (18 Da, Ligand)
- Nb35 (Complex from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- (z)-7-[(1r,2r,3r)-3-hydroxy-2-[(e,3s)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid (352 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Ep2 (Complex from Homo sapiens)
- Prostaglandin e2 receptor ep2 subtype (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (45 kDa, Protein from Homo sapiens)
- Pge2-bound ep2-gs complex (Complex)
- Nanobody-35 (13 kDa, Protein from synthetic construct)
- Gs (Complex from Homo sapiens)
Hyperthermophilic respiratory Complex III
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6kls
Q-score: 0.515
Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F
Angew Chem Int Ed Engl (2020) 59 pp. 343-351 [ DOI: doi:10.1002/anie.201911554 Pubmed: 31778296 ]
- Cytochrome c (27 kDa, Protein from Aquifex aeolicus (strain VF5))
- The cytochrome bc1 complex (respiratory complex iii) (Complex from Aquifex aeolicus)
- 2-[(2~{e},6~{e},10~{z},14~{z},18~{z},23~{r})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione (639 Da, Ligand)
- Cytochrome b subunit (47 kDa, Protein from Aquifex aeolicus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Rieske-i iron sulfur protein (19 kDa, Protein from Aquifex aeolicus (strain VF5))
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
Hyperthermophilic respiratory Complex III
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6klv
Q-score: -0.007
Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F
Angew Chem Int Ed Engl (2020) 59 pp. 343-351 [ DOI: doi:10.1002/anie.201911554 Pubmed: 31778296 ]
- Cytochrome c (27 kDa, Protein from Aquifex aeolicus (strain VF5))
- The cytochrome bc1 complex (respiratory complex iii) (Complex from Aquifex aeolicus)
- 2-[(2~{e},6~{e},10~{z},14~{z},18~{z},23~{r})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione (639 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Rieske-i iron sulfur protein (19 kDa, Protein from Aquifex aeolicus (strain VF5))
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Antimycin (534 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Cytochrome b (47 kDa, Protein from Aquifex aeolicus)