Cryo-EM structure of ET-1 bound ETBR-DNGI complex
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8xwp
Q-score: 0.454
Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T
Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (29 kDa, Protein from Mus musculus)
- Et-1 bound etbr-gi complex (Complex from Homo sapiens)
- Endothelin receptor type b (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)
- Endothelin-1 (2 kDa, Protein from Homo sapiens)
Cryo-EM structure of ET-1 bound ETBR-DNGI complex
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8xwq
Q-score: 0.29
Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T
Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (29 kDa, Protein from Mus musculus)
- Et-1 bound etbr-gi complex (Complex from Homo sapiens)
- Endothelin receptor type b (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)
- Endothelin-1 (2 kDa, Protein from Homo sapiens)
Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8zrt
Q-score: 0.443
Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T
Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]
- Endothelin-1 (2 kDa, Protein from Homo sapiens)
- Et-1 bound etbr complex (Complex from Homo sapiens)
- Endothelin receptor type b (38 kDa, Protein from Homo sapiens)
PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Resolution: 1.92 Å
EM Method: Single-particle
Fitted PDBs: 8wey
Q-score: 0.662
Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, Nagao R
PNAS (2024) 121 pp. e2319658121-e2319658121 [ DOI: doi:10.1073/pnas.2319658121 Pubmed: 38442179 ]
- Psi-lhci (550 kDa, Complex from Cyanidium caldarium)
- Photosystem i reaction center subunit x (7 kDa, Protein from Cyanidium caldarium)
- Beta-carotene (536 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanidium caldarium)
- Lhcr3 (23 kDa, Protein from Cyanidium caldarium)
- Unknown ligand (Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanidium caldarium)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanidium caldarium)
- Zeaxanthin (568 Da, Ligand)
- Lhcr2 (24 kDa, Protein from Cyanidium caldarium)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanidium caldarium)
- Phylloquinone (450 Da, Ligand)
- Lhcr1 (24 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanidium caldarium)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i subunit o (16 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a isomer (893 Da, Ligand)
Mouse apoferritin, Dataset B taken with CRYO ARM 300
Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K
Communications chemistry (2023) 6 [ DOI: 10.1038/s42004-023-00900-x Pubmed: 37258702 ]
Image sets:
Mouse apoferritin, Dataset A taken with CRYO ARM 300
Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K
Communications chemistry (2023) 6 [ DOI: 10.1038/s42004-023-00900-x Pubmed: 37258702 ]
Image sets:
Single-particle cryo-EM structure of mouse apoferritin at 1.49 Angstrom resolution (Dataset B)
Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K
Commun Chem (2023) 6 pp. 98-98 [ Pubmed: 37258702 DOI: doi:10.1038/s42004-023-00900-x ]
- Apoferritin (Complex from Mus musculus)
- Ferritin heavy chain (Protein from Mus musculus)
Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
Resolution: 1.19 Å
EM Method: Single-particle
Fitted PDBs: 8j5a
Q-score: 0.944
Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K
Commun Chem (2023) 6 pp. 98-98 [ Pubmed: 37258702 DOI: doi:10.1038/s42004-023-00900-x ]
- Ferritin heavy chain (20 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Apoferritin from mus musculus (Complex from Mus musculus)
- Sodium ion (22 Da, Ligand)
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8hla
Q-score: 0.577
Himiyama T, Hamaguchi T, Yonekura K, Nakamura T
Bioconjug.Chem. (2023) [ Pubmed: 36888722 DOI: doi:10.1021/acs.bioconjchem.3c00057 ]
- Naph@mix (300 kDa, Complex from Thermococcus kodakarensis)
Structure of the Anabaena PSI-monomer-IsiA supercomplex
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 7y3f
Q-score: 0.526
Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, Shen JR
Nat Commun (2023) 14 pp. 920-920 [ Pubmed: 36805598 DOI: doi:10.1038/s41467-023-36504-1 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp.)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp.)
- Unknown (6 kDa, Protein from Nostoc sp.)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Nostoc sp.)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp.)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psam (4 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp.)
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp.)
- Psi-monomer-isia (640 kDa, Complex from Nostoc sp.)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Nostoc sp.)
- Phylloquinone (450 Da, Ligand)
- Isia (27 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp.)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit xi (51 kDa, Protein from Nostoc sp.)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp.)