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 [ DOI: doi:10.1038/s41467-025-56903-w Pubmed: 39952931 ]
- (2~{s})-2-azanyl-3-[4-[bis(2-chloroethyl)amino]phenyl]propanoic acid (305 Da, Ligand)
- Lat1-cd98hc-fab170 (173 kDa, Complex from Homo sapiens)
- 4f2 cell-surface antigen heavy chain (68 kDa, Protein from Homo sapiens)
- Large neutral amino acids transporter small subunit 1 (56 kDa, Protein from Homo sapiens)
Cryo-EM structure of PsBphP in Pr state
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers FL
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
Cryo-EM structure of PsBphP in Pfr state, Dimer of Dimers PSM only
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
Cryo-EM structure of PsBphP in Pfr state, medial PSM only
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
Cryo-EM structure of PsBphP in Pfr state, splayed PSM only
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
Cryo-EM structure of PsBphP in Pr state, extended DHp
Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD
Nat Commun (2024) 15 pp. 6853-6853 [ DOI: doi:10.1038/s41467-024-50412-y Pubmed: 39127720 ]
- 3-[2-[(z)-[3-(2-carboxyethyl)-5-[(z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(z)-[(3e)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1h-pyrrol-3- yl]propanoic acid (585 Da, Ligand)
- Psbphp (Complex from Pseudomonas syringae pv. tomato str. DC3000)
- Histidine kinase (82 kDa, Protein from Pseudomonas syringae pv. tomato str. DC3000)
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 [ DOI: doi:10.1038/s41467-024-49484-7 Pubmed: 38877016 ]
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- (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)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- Water (18 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 [ DOI: doi:10.1038/s41467-024-49484-7 Pubmed: 38877016 ]
- Phospho-n-acetylmuramoyl-pentapeptide-transferase (40 kDa, Protein from Aquifex aeolicus VF5)
- Mrayaa nanobody (15 kDa, Protein from Lama glama)
- Complex of mray aa dimer with nanobody bound (200 kDa, Complex from Aquifex aeolicus VF5)
- (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)
- Water (18 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) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Human gpr34-gi complex bound to s3e-lysops (Complex)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus norvegicus)
- Probable g-protein coupled receptor 34 (Complex from Homo sapiens)
- Scfv16 (27 kDa, Protein from Mus musculus)
- (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)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
- 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)/g(s)/g(o) subunit gamma-2 (Complex from Bos taurus)
- Scfv16 (Complex from Mus musculus)
- 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 (45 kDa, Protein from Homo sapiens)