Structure of LAT1-CD98hc-Fab170 in complex with BCH, consensus map
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8kdg
Q-score: 0.424
Lee Y, Jin C, Ohgaki R, Xu M, Ogasawara S, Warshamanage R, Yamashita K, Murshudov G, Nureki O, Murata T, Kanai Y
Nat Commun (2025) 16 pp. 1635-1635 [ Pubmed: 39952931 DOI: doi:10.1038/s41467-025-56903-w ]
- Fab170 (Complex from Mus musculus)
- Fab170 light chain (24 kDa, Protein from Mus musculus)
- (1~{s},2~{r},4~{r})-2-azanylbicyclo[2.2.1]heptane-2-carboxylic acid (155 Da, Ligand)
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- Lat1-cd98hc-fab170 (173 kDa, Complex)
- Fab170 heavy chain (24 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lat1-cd98hc (Complex from Homo sapiens)
- Large neutral amino acids transporter small subunit 1 (56 kDa, Protein from Homo sapiens)
Structure of LAT1-CD98hc in complex with BCH, focused on TMD
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8kdh
Q-score: 0.45
Lee Y, Jin C, Ohgaki R, Xu M, Ogasawara S, Warshamanage R, Yamashita K, Murshudov G, Nureki O, Murata T, Kanai Y
Nat Commun (2025) 16 pp. 1635-1635 [ Pubmed: 39952931 DOI: doi:10.1038/s41467-025-56903-w ]
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- (1~{s},2~{r},4~{r})-2-azanylbicyclo[2.2.1]heptane-2-carboxylic acid (155 Da, Ligand)
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Large neutral amino acids transporter small subunit 1 (56 kDa, Protein from Homo sapiens)
- Lat1-cd98hc-fab170 (173 kDa, Complex from Homo sapiens)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8y1v
Q-score: 0.333
To Be Published
- Isoform 6 of glutamate receptor ionotropic, nmda 1 (97 kDa, Protein from Homo sapiens)
- N-methyl-d-aspartate receptors (400 MDa, Complex from Homo sapiens)
- Glutamate receptor ionotropic, nmda 2d (99 kDa, Protein from Homo sapiens)
- (2~{r},3~{s},4~{s},5~{r},6~{r})-2-(hydroxymethyl)-6-[(2~{s})-2-methyl-4-[(1~{r},2~{r},4~{s},6~{s},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s},18~{r})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol (592 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9eqg
Q-score: 0.627
Lyu Q, Xue W, Liu R, Ma Q, Kasaragod VB, Sun S, Li Q, Chen Y, Yuan M, Yang Y, Zhang B, Nie A, Jia S, Shen C, Gao P, Rong W, Yu C, Bi Y, Zhang C, Nan F, Ning G, Rao Z, Yang X, Wang J, Wang W
Nature (2024) 634 pp. 936-943 [ Pubmed: 39261733 DOI: doi:10.1038/s41586-024-07929-5 ]
- Hexadecane (226 Da, Ligand)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Hexane (86 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (56 kDa, Protein from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit alpha-1 (52 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Water (18 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Cryoem structure of human full-length alpha1beta3gamma2l gaba(a)r in complex with gaba and puerarin (250 kDa, Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Decane (142 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)
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Puerarin (416 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Structure of wild type human PSS1
Long T, Li D, Vale G, Jiang Y, Schmiege P, Yang ZJ, McDonald JG, Li X
Cell (2024) 187 pp. 5665-5678.e18 [ Pubmed: 39208797 DOI: doi:10.1016/j.cell.2024.08.004 ]
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Water (18 Da, Ligand)
- (2r)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate (811 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Phosphatidylserine synthase 1 (48 kDa, Protein from Homo sapiens)
- Pss1 (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
Structure of inhibitor-bound human PSS1
Long T, Li D, Vale G, Jiang Y, Schmiege P, Yang ZJ, McDonald JG, Li X
Cell (2024) 187 pp. 5665-5678.e18 [ Pubmed: 39208797 DOI: doi:10.1016/j.cell.2024.08.004 ]
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Water (18 Da, Ligand)
- Inhibitor-bound human pss1 (Complex from Homo sapiens)
- (7p)-7-[(4s)-4-{4-[3,5-bis(trifluoromethyl)phenoxy]phenyl}-5-(2,2-difluoropropyl)-6-oxo-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazol-3-yl]-1,3-benzoxazol-2(3h)-one (638 Da, Ligand)
- (2r)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate (811 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Phosphatidylserine synthase 1 (48 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
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)