Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A - Conformation A
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 9f33
Q-score: 0.528
Arroyo-Urea S, Nazarova AL, Carrion-Antoli A, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, Garcia-Nafria J
Nat Commun (2024) 15 pp. 7759-7759 [ DOI: doi:10.1038/s41467-024-51993-4 Pubmed: 39237617 ]
- Guanine nucleotide-binding protein g(o) subunit alpha (40 kDa, Protein from Homo sapiens)
- Green fluorescent protein,d(3) dopamine receptor (74 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- N-[2-[(1r,2s)-2-[[(2s,5s)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-1h-indole-2-carboxamide (433 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Rattus norvegicus)
- D3r:go protein complex with bitopic fob02-04a-conformation a (190 kDa, Complex from Homo sapiens)
- Antibody scfv16 (28 kDa, Protein from Mus musculus)
Cryo-EM structure of Dopamine 3 receptor:Go complex bound to bitopic FOB02-04A - Conformation B
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 9f34
Q-score: 0.456
Arroyo-Urea S, Nazarova AL, Carrion-Antoli A, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, Garcia-Nafria J
Nat Commun (2024) 15 pp. 7759-7759 [ DOI: doi:10.1038/s41467-024-51993-4 Pubmed: 39237617 ]
- Guanine nucleotide-binding protein g(o) subunit alpha (40 kDa, Protein from Homo sapiens)
- Green fluorescent protein,d(3) dopamine receptor (74 kDa, Protein from Homo sapiens)
- Antibody scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- N-[2-[(1r,2s)-2-[[(2s,5s)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-1h-indole-2-carboxamide (433 Da, Ligand)
- D3r: gtrimer: scfv16 complex bound to the bitopic fob02-04a - conformation b (190 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Rattus norvegicus)
TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8t0c
Q-score: 0.457
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- (2r)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate (382 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 1 (92 kDa, Protein from Rattus norvegicus)
- Trpv1 in nanodisc bound with lysophosphatidic acid in all four monomers (688 kDa, Complex from Rattus norvegicus)
- Sodium ion (22 Da, Ligand)
TRPV1 in Nanodisc not bound with lysophosphatidic acid (apo)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8t0e
Q-score: 0.462
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- Sodium ion (22 Da, Ligand)
- (2r)-3-{[(r)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate (867 Da, Ligand)
- Trpv1 in nanodisc, no lysophosphatidic acid bound (688 kDa, Complex from Rattus norvegicus)
- Transient receptor potential cation channel subfamily v member 1 (92 kDa, Protein from Rattus norvegicus)
- Water (18 Da, Ligand)
TRPV1 in nanodisc bound with one LPA in one monomer
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8t0y
Q-score: 0.471
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- (2r)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate (382 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- (2r)-3-{[(r)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate (867 Da, Ligand)
- Trpv1 in nanodisc bound with one lpa in one monomer (688 kDa, Complex from Rattus norvegicus)
- Transient receptor potential cation channel subfamily v member 1 (92 kDa, Protein from Rattus norvegicus)
TRPV1 in nanodisc bound with two LPA molecules in opposite monomers
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8t10
Q-score: 0.392
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- (2r)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate (382 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- (2r)-3-{[(r)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate (867 Da, Ligand)
- Trpv1 in nanodisc bound with two lpa molecules in opposite monomers (688 kDa, Complex from Rattus norvegicus)
- Transient receptor potential cation channel subfamily v member 1 (92 kDa, Protein from Rattus norvegicus)
TRPV1 in nanodisc bound with 2 LPA molecules in neighboring monomers
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8t3l
Q-score: 0.47
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- (2r)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate (382 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 1 (73 kDa, Protein from Rattus norvegicus)
- (2r)-3-{[(r)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate (867 Da, Ligand)
- Trpv1 in nanodisc bound with 2 lpa molecules in neighboring monomers (688 kDa, Complex from Rattus norvegicus)
TRPV1 in nanodisc bound with 3 LPA molecules
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8t3m
Q-score: 0.447
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- (2r)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate (382 Da, Ligand)
- [(2~{r})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{s},3~{s},5~{r},6~{s})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate (811 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 1 (73 kDa, Protein from Rattus norvegicus)
- Trpv1 in nanodisc bound with 2 lpa molecules in neighboring monomers (688 kDa, Complex from Rattus norvegicus)
TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8u2z
Q-score: 0.447
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- [(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)
- Water (18 Da, Ligand)
- Trpv1 in nanodisc bound with dic8-pip2 in the dilated state (688 kDa, Complex from Rattus norvegicus)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 1 (72 kDa, Protein from Rattus norvegicus)
TRPV1 in nanodisc bound with diC8-PIP2 in the closed state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8u30
Q-score: 0.544
Arnold WR, Mancino A, Moss 3rd FR, Frost A, Julius D, Cheng Y
Nat Struct Mol Biol (2024) 31 pp. 1377-1385 [ DOI: doi:10.1038/s41594-024-01299-2 Pubmed: 38698206 ]
- [(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)
- Trpv1 in nanodisc bound with dic8-pip2 in the dilated state (688 kDa, Complex from Rattus norvegicus)
- Sodium ion (22 Da, Ligand)
- Transient receptor potential cation channel subfamily v member 1 (92 kDa, Protein from Rattus norvegicus)
- Water (18 Da, Ligand)