Cryo-EM structure of Light-harvesting complex from Spinacia oleracea
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8y15
Q-score: 0.709
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ DOI: doi:10.1093/pnasnexus/pgae405 Pubmed: 39346626 ]
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- Water (18 Da, Ligand)
- Light-harvesting complex ii from spinacia oleracea (700 kDa, Complex from Spinacia oleracea)
- Lutein (568 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yee
Q-score: 0.678
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ DOI: doi:10.1093/pnasnexus/pgae405 Pubmed: 39346626 ]
- Water (18 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- In vitro reconstituted light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
- Chlorophyll a (893 Da, Ligand)
Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O
Electrochim Acta (2024) 490 [ DOI: doi:10.1016/j.electacta.2024.144271 ]
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase (h1147a) large subunit (59 kDa, Protein from Gluconobacter japonicus)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- D-fructose dehydrogenase (h1147a) from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O
Electrochim Acta (2024) 490 [ DOI: doi:10.1016/j.electacta.2024.144271 ]
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- D-fructose dehydrogenase (n1146a) from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fructose dehydrogenase (n1146a) large subunit (59 kDa, Protein from Gluconobacter japonicus)
- Fe3-s4 cluster (295 Da, Ligand)
Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O
Electrochim Acta (2024) 490 [ DOI: doi:10.1016/j.electacta.2024.144271 ]
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- D-fructose dehydrogenase (n1146q) from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- Fructose dehydrogenase large subunit (59 kDa, Protein from Gluconobacter japonicus)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
Fukawa E, Suzuki Y, Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Sowa K, Kitazumi Y, Shirai O
Electrochim Acta (2024) 490 [ DOI: doi:10.1016/j.electacta.2024.144271 ]
- D-fructose dehydrogenase (n1190a) from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase large subunit (59 kDa, Protein from Gluconobacter japonicus)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8jej
Q-score: 0.653
Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
ACS Catal (2023) 13 [ DOI: doi:10.1021/acscatal.3c03769 ]
- D-fructose dehydrogenase from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Fructose dehydrogenase large subunit (59 kDa, Protein from Gluconobacter japonicus)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8jek
Q-score: 0.619
Suzuki Y, Makino F, Miyata T, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
ACS Catal (2023) 13 [ DOI: doi:10.1021/acscatal.3c03769 ]
- D-fructose dehydrogenase from gluconobacter japonicus (140 kDa, Complex from Gluconobacter japonicus)
- Fructose dehydrogenase small subunit (20 kDa, Protein from Gluconobacter japonicus)
- Ubiquinone-10 (863 Da, Ligand)
- Fructose dehydrogenase cytochrome subunit (52 kDa, Protein from Gluconobacter japonicus)
- Heme c (618 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Fructose dehydrogenase large subunit (59 kDa, Protein from Gluconobacter japonicus)
Cryo-EM Structure of Membrane-Bound Alcohol Dehydrogenase from Gluconobacter oxydans
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8gy2
Q-score: 0.615
Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
ACS Catal (2023) 13 pp. 7955-7965 [ DOI: doi:10.1021/acscatal.3c01962 ]
- Ubiquinone-10 (863 Da, Ligand)
- Alcohol dehydrogenase (quinone), dehydrogenase subunit (82 kDa, Protein from Gluconobacter oxydans 621H)
- Alcohol dehydrogenase (quinone), cytochrome c subunit (51 kDa, Protein from Gluconobacter oxydans 621H)
- Alcohol dehydrogenase from gluconobacter oxydans (150 kDa, Complex from Gluconobacter oxydans)
- Small subunit of alcohol dehydrogenase (14 kDa, Protein from Gluconobacter oxydans)
- Pyrroloquinoline quinone (330 Da, Ligand)
- Heme c (618 Da, Ligand)
- Calcium ion (40 Da, Ligand)
Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8gy3
Q-score: 0.588
Adachi T, Miyata T, Makino F, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
ACS Catal (2023) 13 pp. 7955-7965 [ DOI: doi:10.1021/acscatal.3c01962 ]
- Ubiquinone-10 (863 Da, Ligand)
- Small subunit of aldehyde dehydrogenase (16 kDa, Protein from Gluconobacter oxydans)
- Cytochrome c subunit of aldehyde dehydrogenase (48 kDa, Protein from Gluconobacter oxydans)
- Large subunit of aldehyde dehydrogenase (83 kDa, Protein from Gluconobacter oxydans)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- (molybdopterin-cytosine dinucleotide-s,s)-dioxo-aqua-molybdenum(v) (844 Da, Ligand)
- Aldehyde dehydrogenase from gluconobacter oxydans (150 kDa, Complex from Gluconobacter oxydans)