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 ]
- Photosystem i reaction center subunit x (7 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanidium caldarium)
- Beta-carotene (536 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Cyanidium caldarium)
- Lhcr3 (23 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanidium caldarium)
- Unknown ligand (Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{r} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol (568 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanidium caldarium)
- Psi-lhci (550 kDa, Complex from Cyanidium caldarium)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a (893 Da, Ligand)
- Lhcr2 (24 kDa, Protein from Cyanidium caldarium)
- Water (18 Da, Ligand)
- Photosystem i subunit o (16 kDa, Protein from Cyanidium caldarium)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanidium caldarium)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lhcr1 (24 kDa, Protein from Cyanidium caldarium)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 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 [ DOI: doi:10.1038/s42004-023-00900-x Pubmed: 37258702 ]
- Ferritin heavy chain (Protein from Mus musculus)
- Apoferritin (Complex 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 [ DOI: doi:10.1038/s42004-023-00900-x Pubmed: 37258702 ]
- Water (18 Da, Ligand)
- Ferritin heavy chain (20 kDa, Protein from Mus musculus)
- Sodium ion (22 Da, Ligand)
- Apoferritin from mus musculus (Complex from Mus musculus)
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 reaction center subunit ix (5 kDa, Protein from Nostoc sp.)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Nostoc sp.)
- Phylloquinone (450 Da, Ligand)
- Psam (4 kDa, Protein from Nostoc sp.)
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp.)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp.)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Isia (27 kDa, Protein from Nostoc sp.)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit xi (51 kDa, Protein from Nostoc sp.)
- Unknown (6 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp.)
- Water (18 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp.)
- Psi-monomer-isia (640 kDa, Complex from Nostoc sp.)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp.)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of Beta-galactosidase at 1.57A resolution
To Be Published
- Beta-galactosidase (466 kDa, Complex from Escherichia coli)
Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7vea
Q-score: 0.415
Kawakami K, Hamaguchi T, Hirose Y, Kosumi D, Miyata M, Kamiya N, Yonekura K
Nat Commun (2022) 13 pp. 3389-3389 [ DOI: doi:10.1038/s41467-022-30962-9 Pubmed: 35715389 ]
- Phycocyanobilin (588 Da, Ligand)
- Phycobiliprotein apce (127 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Phycobilisome core component (18 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Phycobilisome core complex from thermosynechococcus vulcanus (Complex from Thermosynechococcus vulcanus NIES-2134)
- Allophycocyanin beta chain (17 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Allophycocyanin alpha chain (17 kDa, Protein from Thermosynechococcus vestitus BP-1)
Phycocyanin rod structure of cyanobacterial phycobilisome
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7veb
Q-score: 0.343
Kawakami K, Hamaguchi T, Hirose Y, Kosumi D, Miyata M, Kamiya N, Yonekura K
Nat Commun (2022) 13 pp. 3389-3389 [ Pubmed: 35715389 DOI: doi:10.1038/s41467-022-30962-9 ]
- Phycobilisome 8.9 kda linker polypeptide, phycocyanin-associated, rod (8 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Phycobilisome rod-core linker polypeptide cpcg2 (28 kDa, Protein from Thermosynechococcus elongatus BP-1)
- C-phycocyanin alpha subunit (17 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (32 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Phycocyanin rod complex of cyanobacterial phyocobilisome (Complex from Thermosynechococcus vulcanus NIES-2134)
- Phycocyanobilin (588 Da, Ligand)
- C-phycocyanin beta subunit (18 kDa, Protein from Thermosynechococcus elongatus BP-1)