Cryo-EM structure of Nav1.7 with LCM
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s9b
Q-score: 0.513
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- Sodium channel protein type 9 subunit alpha (226 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Sodium channel subunit beta-2 (24 kDa, Protein from Homo sapiens)
- Lacosamide (250 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)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 with beta subunits (Complex 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 Nav1.7 with CBZ
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8s9c
Q-score: 0.5
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- Sodium channel protein type 9 subunit alpha (226 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 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)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human voltage-gated sodium channel nav1.7 with beta subunits (Complex from Homo sapiens)
- Benzo[b][1]benzazepine-11-carboxamide (236 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of human Nav1.7 in complex with bupivacaine
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8i5b
Q-score: 0.507
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- 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)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- Levobupivacaine (288 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human nav1.7 in complex with bupivacaine (250 kDa, Complex from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (230 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of human Nav1.7 in complex with PF-05089771
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8i5g
Q-score: 0.516
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- Sodium channel protein type 9 subunit alpha (226 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Sodium channel subunit beta-1 (21 kDa, Protein from Homo sapiens)
- 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)
- Sodium ion (22 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human nav1.7 in complex with bupivacaine (250 kDa, Complex from Homo sapiens)
- Pf-05089771 (500 Da, Ligand)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of human Nav1.7 in complex with Vinpocetine
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8i5x
Q-score: 0.477
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- 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 nav1.7 in complex with vinpocetine (250 kDa, 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)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Vinpocetine (350 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (230 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of human Nav1.7 in complex with vixotrigine
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8i5y
Q-score: 0.531
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- Vixotrigine (314 Da, Ligand)
- 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)
- (2s,3r,4e)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (421 Da, Ligand)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human nav1.7 in complex with vixotrigine (250 kDa, Complex from Homo sapiens)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (230 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of human Nav1.7 in complex with Hardwickii acid
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8j4f
Q-score: 0.501
Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N
Nat Commun (2023) 14 pp. 3224-3224 [ DOI: doi:10.1038/s41467-023-38942-3 Pubmed: 37270609 ]
- Human nav1.7 in complex with hardwickii acid (250 kDa, Complex from Homo sapiens)
- (3beta,14beta,17beta,25r)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en (544 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Sodium channel subunit beta-1 (24 kDa, Protein from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- (4~{a}~{r},5~{s},6~{r},8~{a}~{r})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid (316 Da, Ligand)
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (230 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of PDF-2180 Spike glycoprotein
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7u6r
Q-score: 0.63
Xiong Q, Cao L, Ma C, Tortorici MA, Liu C, Si J, Liu P, Gu M, Walls AC, Wang C, Shi L, Tong F, Huang M, Li J, Zhao C, Shen C, Chen Y, Zhao H, Lan K, Corti D, Veesler D, Wang X, Yan H
Nature (2022) 612 pp. 748-757 [ Pubmed: 36477529 DOI: doi:10.1038/s41586-022-05513-3 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pdf-2180 spike glycoprotein (147 kDa, Protein from Bat coronavirus)
- Predict/pdf-2180 (Virus from PREDICT/PDF-2180)
Structure of NeoCOV RBD binding to Bat37 ACE2
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7wpo
Q-score: 0.458
Xiong Q, Cao L, Ma C, Tortorici MA, Liu C, Si J, Liu P, Gu M, Walls AC, Wang C, Shi L, Tong F, Huang M, Li J, Zhao C, Shen C, Chen Y, Zhao H, Lan K, Corti D, Veesler D, Wang X, Yan H
Nature (2022) 612 pp. 748-757 [ Pubmed: 36477529 DOI: doi:10.1038/s41586-022-05513-3 ]
- Spike glycoprotein (21 kDa, Protein from Coronavirus Neoromicia/PML-PHE1/RSA/2011)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme (80 kDa, Protein from Pipistrellus pipistrellus)
- Neocov rbd-bat37 ace2 complex (Complex from Coronavirus Neoromicia/PML-PHE1/RSA/2011)
Structure of PDF-2180-COV RBD binding to Bat37 ACE2
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7wpz
Q-score: 0.427
Xiong Q, Cao L, Ma C, Tortorici MA, Liu C, Si J, Liu P, Gu M, Walls AC, Wang C, Shi L, Tong F, Huang M, Li J, Zhao C, Shen C, Chen Y, Zhao H, Lan K, Corti D, Veesler D, Wang X, Yan H
Nature (2022) 612 pp. 748-757 [ Pubmed: 36477529 DOI: doi:10.1038/s41586-022-05513-3 ]
- Pdf-2180-cov rbd-bat37 ace2 complex (Complex from Bat coronavirus)
- Spike glycoprotein (22 kDa, Protein from Bat coronavirus)
- Angiotensin-converting enzyme (69 kDa, Protein from Pipistrellus pipistrellus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)