Structure of LAT1-CD98hc in complex with melphalan, focused on TMD
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8kdo
Q-score: 0.417
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 ]
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- (2~{s})-2-azanyl-3-[4-[bis(2-chloroethyl)amino]phenyl]propanoic acid (305 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)
Cryo-EM structure of MraY in complex with analogue 2
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9b70
Q-score: 0.561
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ Pubmed: 38877016 DOI: doi:10.1038/s41467-024-49484-7 ]
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{s})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid (934 Da, Ligand)
Cryo-EM structure of MraY in complex with analogue 3
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b71
Q-score: 0.585
Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S
Nat Commun (2024) 15 pp. 5085-5085 [ Pubmed: 38877016 DOI: doi:10.1038/s41467-024-49484-7 ]
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 Da, Ligand)
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- (2~{s},3~{s})-3-[(2~{s},3~{r},4~{s},5~{r})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{s},3~{s},4~{r},5~{r})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{s})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid (962 Da, Ligand)
Human GPR34 -Gi complex bound to S3E-LysoPS
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8xbe
Q-score: 0.445
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to s3e-lysops (Complex)
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[(~{z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (551 Da, Ligand)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 8xbg
Q-score: 0.42
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- Human gpr34-gi complex bound to s3e-lysops, receptor focused (Complex from Homo sapiens)
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[(~{z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (551 Da, Ligand)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
Human GPR34 -Gi complex bound to M1
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8xbh
Q-score: 0.473
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to m1 (Complex)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (617 Da, Ligand)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
Human GPR34 -Gi complex bound to M1, receptor focused
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8xbi
Q-score: 0.457
Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O
Nat Commun (2024) 15 pp. 902-902 [ DOI: doi:10.1038/s41467-024-45046-z Pubmed: 38326347 ]
- (2~{s})-2-azanyl-3-[[(2~{r})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid (617 Da, Ligand)
- Probable g-protein coupled receptor 34 (45 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to m1,receptor focused (Complex from Homo sapiens)
Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8oxa
Q-score: 0.546
Dieudonne T, Kummerer F, Laursen MJ, Stock C, Flygaard RK, Khalid S, Lenoir G, Lyons JA, Lindorff-Larsen K, Nissen P
Nat Commun (2023) 14 pp. 7492-7492 [ DOI: doi:10.1038/s41467-023-42828-9 Pubmed: 37980352 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Oxido(dioxo)vanadium (98 Da, Ligand)
- Cell cycle control protein 50a (41 kDa, Protein from Homo sapiens)
- (2~{s})-2-azanyl-3-[[(2~{r})-3-hexadecanoyloxy-2-[(~{z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid (762 Da, Ligand)
- Atp8b1-cdc50a complex (185 kDa, Complex from Homo sapiens)
- Phospholipid-transporting atpase ic (136 kDa, Protein from Homo sapiens)
Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7xv3
Q-score: 0.579
Liang J, Inoue A, Ikuta T, Xia R, Wang N, Kawakami K, Xu Z, Qian Y, Zhu X, Zhang A, Guo C, Huang Z, He Y
Nat Commun (2023) 14 pp. 1012-1012 [ DOI: doi:10.1038/s41467-023-36575-0 Pubmed: 36823105 ]
- Water (18 Da, Ligand)
- (2~{s})-2-$l^{4}-azanyl-3-[[(2~{r})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid (497 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Engineered g protein subunit s (mini-gs) (41 kDa, Protein from Homo sapiens)
- Probable g-protein coupled receptor 174 (38 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Nb35 (17 kDa, Protein from Lama glama)
- Gpr174/gs complex (Complex from Homo sapiens)