Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdv
Q-score: 0.658
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY
Commun Biol (2024) 7 pp. 176-176 [ DOI: doi:10.1038/s42003-024-05863-w Pubmed: 38347078 ]
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Bacteriochlorophyll a (911 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Spirilloxanthin (596 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Magnesium ion (24 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Calcium ion (40 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 3.9 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x54
Q-score: 0.375
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cbg-parm filament with adp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP and a short incubation time
Resolution: 8.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x55
Q-score: 0.168
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x56
Q-score: 0.486
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Cbg-parm filament with gdp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP or GDPPi
Resolution: 6.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x59
Q-score: 0.189
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cbg-parm filament with gtp or gdppi (Complex from Clostridium botulinum)
Cryo-EM structure of phosphoketolase from Bifidobacterium longum
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 6lxv
Q-score: 0.763
Nakata K, Miyazaki N, Yamaguchi H, Hirose M, Kashiwagi T, Kutumbarao NHV, Miyashita O, Tama F, Miyano H, Mizukoshi T, Iwasaki K
J Struct Biol (2022) 214 pp. 107842-107842 [ DOI: doi:10.1016/j.jsb.2022.107842 Pubmed: 35181457 ]
- Thiamine diphosphate (425 Da, Ligand)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Phosphoketolase with thiamine-diphophate (Complex from Bifidobacterium longum subsp. longum F8)
- Phosphoketolase (93 kDa, Protein from Bifidobacterium longum subsp. longum F8)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6klo
Q-score: 0.586
Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H
Nat Struct Mol Biol (2020) 27 pp. 288-296 [ Pubmed: 32123390 DOI: doi:10.1038/s41594-020-0388-6 ]
- Complex structure of iota toxin enzymatic component (ia) and binding component (ib) pore with short stem (570 kDa, Complex from Clostridium perfringens)
- Calcium ion (40 Da, Ligand)
- Iota toxin component ib (74 kDa, Protein from Clostridium perfringens)
- Iota toxin component ia (48 kDa, Protein from Clostridium perfringens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6klw
Q-score: 0.572
Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H
Nat Struct Mol Biol (2020) 27 pp. 288-296 [ Pubmed: 32123390 DOI: doi:10.1038/s41594-020-0388-6 ]
- Complex structure of iota toxin enzymatic component (ia) and binding component (ib) pore with long stem (570 kDa, Complex from Clostridium perfringens)
- Calcium ion (40 Da, Ligand)
- Iota toxin component ib (74 kDa, Protein from Clostridium perfringens)
- Iota toxin component ia (48 kDa, Protein from Clostridium perfringens)
Pore structure of Iota toxin binding component (Ib)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6klx
Q-score: 0.596
Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H
Nat Struct Mol Biol (2020) 27 pp. 288-296 [ Pubmed: 32123390 DOI: doi:10.1038/s41594-020-0388-6 ]
- Iota toxin component ib (74 kDa, Protein from Clostridium perfringens)
- Calcium ion (40 Da, Ligand)
- Pore structure of iota toxin binding component (ib) (520 kDa, Complex from Clostridium perfringens)
Cryo-EM structure of T=3 Penaeus vannamei nodavirus
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ab6
Q-score: 0.505
Chen NC, Yoshimura M, Miyazaki N, Guan HH, Chuankhayan P, Lin CC, Chen SK, Lin PJ, Huang YC, Iwasaki K, Nakagawa A, Chan SI, Chen CJ
Commun Biol (2019) 2 pp. 72-72 [ DOI: doi:10.1038/s42003-019-0311-z Pubmed: 30820467 ]
- Calcium ion (40 Da, Ligand)
- Capsid protein (40 kDa, Protein from Penaeus vannamei nodavirus)
- Penaeus vannamei nodavirus (Virus from Penaeus vannamei nodavirus)