Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G
Nat Struct Mol Biol (2024) 31 pp. 378-389 [ Pubmed: 38326650 DOI: doi:10.1038/s41594-023-01206-1 ]
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Elongin-b (elob), elongin-c (eloc), protein fem-1 homolog c (fem1c) and trapped ube2r2-donor ub-acceptor ub-sil1 peptide (Complex from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Voltage-gated sodium channel Nav1.7 variant M9
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8xmm
Q-score: 0.544
Li Z, Wu Q, Huang G, Jin X, Li J, Pan X, Yan N
PNAS (2024) 121 pp. e2322899121-e2322899121 [ Pubmed: 38381792 DOI: doi:10.1073/pnas.2322899121 ]
- 1-o-octadecyl-sn-glycero-3-phosphocholine (510 Da, Ligand)
- Voltage-gated sodium channel nav1.7-m9 (Complex from Homo sapiens)
- (2s,3r,4e)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate (421 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Sodium channel subunit beta-1 (26 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sodium channel protein type 9 subunit alpha (231 kDa, Protein from Homo sapiens)
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8q7r
Q-score: 0.324
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Ubiquitin ligation to substrate by a cullin-ring e3 ligase & cdc34: nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2~donor ub-sil1 peptide (180 kDa, Complex)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-sil1 peptide (Complex from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Nucleotide exchange factor sil1 (2 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 5-azanyl-1-oxidanyl-pentan-2-one (117 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8r5h
Q-score: 0.394
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Bromodomain-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (25 kDa, Protein from Homo sapiens)
- Ubiquitin ligation to neosubstrate by a cullin-ring e3 ligase and cdc34: nedd8-cul2-rbx1-elob/c-vhl-mz1 with trapped ube2r2~donor ub-brd4 bd2 (190 kDa, Complex from Homo sapiens)
- Von hippel-lindau disease tumor suppressor (18 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- (2~{s},4~{r})-1-[(2~{s})-2-[2-[2-[2-[2-[2-[(9~{s})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{n}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide (1 kDa, Ligand)
- Cdc34, nedd8, elob, eloc, vhl, brd4 with ube2r2-donor ub- brd4 bd2 (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8pql
Q-score: 0.431
Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G
Nat Struct Mol Biol (2024) 31 pp. 378-389 [ Pubmed: 38326650 DOI: doi:10.1038/s41594-023-01206-1 ]
- 5-azanylpentan-2-one (101 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
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 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)