Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdu
Q-score: 0.676
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: 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)
Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1
Resolution: 21.0 Å
EM Method: Single-particle
Fitted PDBs: 5gje
Q-score: 0.027
Matoba K, Mihara E, Tamura-Kawakami K, Miyazaki N, Maeda S, Hirai H, Thompson S, Iwasaki K, Takagi J
Cell Rep (2017) 18 pp. 32-40 [ DOI: doi:10.1016/j.celrep.2016.12.017 Pubmed: 28052259 ]
- Phosphate ion (94 Da, Ligand)
- Lrp6 ectodomain (Complex)
- Glycerol (92 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dickkopf-related protein 1 (9 kDa, Protein from Homo sapiens)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Human dickkopf-related protein1 (Complex)
- Low-density lipoprotein receptor-related protein 6 (69 kDa, Protein from Homo sapiens)
- Human lrp6 ectodomain complexed with full length of dkk1 (210 kDa, Complex from Homo sapiens)
- Water (18 Da, Ligand)