Structure of a human glycosylphosphatidylinositol (GPI) transamidase
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7w72
Q-score: 0.568
Zhang H, Su J, Li B, Gao Y, Liu M, He L, Xu H, Dong Y, Zhang XC, Zhao Y
Nat Struct Mol Biol (2022) 29 pp. 203-209 [ DOI: doi:10.1038/s41594-022-00726-6 Pubmed: 35165458 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glycosylphosphatidylinositol anchor attachment 1 protein (67 kDa, Protein from Homo sapiens)
- Gpi transamidase component pig-s (59 kDa, Protein from Homo sapiens)
- Human glycosylphosphatidylinositol transamidase (Complex from Homo sapiens)
- Gpi transamidase component pig-t (60 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- [2-[[(2~{r})-2-hexanoyloxy-3-[(~{e})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{e},4~{e})-hepta-2,4-dienoate (622 Da, Ligand)
- Gpi-anchor transamidase (45 kDa, Protein from Homo sapiens)
- Phosphatidylinositol glycan anchor biosynthesis class u protein (48 kDa, Protein from Homo sapiens)
Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, apo state
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vfs
Q-score: 0.533
Dong Y, Gao Y, Xu S, Wang Y, Yu Z, Li Y, Li B, Yuan T, Yang B, Zhang XC, Jiang D, Huang Z, Zhao Y
Cell Rep (2021) 37 pp. 109931-109931 [ DOI: doi:10.1016/j.celrep.2021.109931 Pubmed: 34731621 ]
- Hexadecane (226 Da, Ligand)
- Voltage-dependent n-type calcium channel subunit alpha-1b (262 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Voltage-dependent l-type calcium channel subunit beta-1 (65 kDa, Protein from Homo sapiens)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (124 kDa, Protein from Homo sapiens)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Cav2.2-alpha2delta1-beta1 complex (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to PD173212
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7vfv
Q-score: 0.49
Dong Y, Gao Y, Xu S, Wang Y, Yu Z, Li Y, Li B, Yuan T, Yang B, Zhang XC, Jiang D, Huang Z, Zhao Y
Cell Rep (2021) 37 pp. 109931-109931 [ DOI: doi:10.1016/j.celrep.2021.109931 Pubmed: 34731621 ]
- Hexadecane (226 Da, Ligand)
- Voltage-dependent n-type calcium channel subunit alpha-1b (262 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Voltage-dependent l-type calcium channel subunit beta-1 (65 kDa, Protein from Homo sapiens)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (124 kDa, Protein from Homo sapiens)
- (2~{s})-~{n}-[(2~{s})-1-(~{tert}-butylamino)-1-oxidanylidene-3-(4-phenylmethoxyphenyl)propan-2-yl]-2-[(4-~{tert}-butylphenyl)methyl-methyl-amino]-4-methyl-pentanamide (599 Da, Ligand)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Cav2.2-alpha2delta1-beta1 complex (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7vfw
Q-score: 0.407
Dong Y, Gao Y, Xu S, Wang Y, Yu Z, Li Y, Li B, Yuan T, Yang B, Zhang XC, Jiang D, Huang Z, Zhao Y
Cell Rep (2021) 37 pp. 109931-109931 [ DOI: doi:10.1016/j.celrep.2021.109931 Pubmed: 34731621 ]
- Hexadecane (226 Da, Ligand)
- Voltage-dependent n-type calcium channel subunit alpha-1b (262 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Voltage-dependent l-type calcium channel subunit beta-1 (65 kDa, Protein from Homo sapiens)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (124 kDa, Protein from Homo sapiens)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Cav2.2-alpha2delta1-beta1 complex (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 5-(4-chlorophenyl)-1-(2-methoxyphenyl)-3-(2,2,6,6-tetramethyloxan-4-yl)pyrazole (424 Da, Ligand)
DNQX-bound GluK2-1xNeto2 complex
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7f59
Q-score: 0.311
He L, Sun J, Gao Y, Li B, Wang Y, Dong Y, An W, Li H, Yang B, Ge Y, Zhang XC, Shi YS, Zhao Y
Nature (2021) 599 pp. 325-329 [ DOI: doi:10.1038/s41586-021-03936-y Pubmed: 34552241 ]
- Neuropilin and tolloid-like protein 2 (59 kDa, Protein from Rattus norvegicus)
- Dnqx-bound gluk2-1xneto2 complex (Complex from Rattus norvegicus)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Glutamate receptor ionotropic, kainate 2 (102 kDa, Protein from Rattus norvegicus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
LBD-TMD focused reconstruction of DNQX-bound GluK2-1xNeto2 complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7f5b
Q-score: 0.405
He L, Sun J, Gao Y, Li B, Wang Y, Dong Y, An W, Li H, Yang B, Ge Y, Zhang XC, Shi YS, Zhao Y
Nature (2021) 599 pp. 325-329 [ DOI: doi:10.1038/s41586-021-03936-y Pubmed: 34552241 ]
- Neuropilin and tolloid-like protein 2 (59 kDa, Protein from Rattus norvegicus)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Glutamate receptor ionotropic, kainate 2 (102 kDa, Protein from Rattus norvegicus)
- Lbd-tmd focused reconstruction of dnqx-bound gluk2-1xneto2 complex (Complex from Rattus norvegicus)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7dsx
Q-score: 0.456
Dong Y, Gao Y, Ilie A, Kim D, Boucher A, Li B, Zhang XC, Orlowski J, Zhao Y
Nat Commun (2021) 12 pp. 3474-3474 [ DOI: doi:10.1038/s41467-021-23496-z Pubmed: 34108458 ]
- Sodium/hydrogen exchanger 1 (57 kDa, Protein from Homo sapiens)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Calcineurin b homologous protein 1 (chp1) under ph 7.5 (Complex)
- Calcineurin b homologous protein 1 (21 kDa, Protein from Homo sapiens)
- Sodium/protein exchanger 1 (nhe1) under ph 7.5, bound by cariporide (182 kDa, Complex from Homo sapiens)
- N-[bis(azanyl)methylidene]-3-methylsulfonyl-4-propan-2-yl-benzamide (283 Da, Ligand)
- Human nhe1-chp1 complex under ph 7.5, bound by cariporide (230 kDa, Complex from Homo sapiens)