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)
Cryo-EM structure of KpFtsZ-monobody double helical tube
Resolution: 2.67 Å
EM Method: Helical reconstruction
Fitted PDBs: 8h1o
Q-score: 0.621
Fujita J, Amesaka H, Yoshizawa T, Hibino K, Kamimura N, Kuroda N, Konishi T, Kato Y, Hara M, Inoue T, Namba K, Tanaka SI, Matsumura H
Nat Commun (2023) 14 pp. 4073-4073 [ Pubmed: 37429870 DOI: doi:10.1038/s41467-023-39807-5 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Monobody (Complex from Homo sapiens)
- Kpftsz (Complex from Klebsiella pneumoniae)
- Cryo-em structure of kpftsz-monobody double helical tube (Complex)
- Mb(ec/kpftsz_s1) (9 kDa, Protein from Homo sapiens)
- Cell division protein ftsz (40 kDa, Protein from Klebsiella pneumoniae)
Cryo-EM structure of KpFtsZ single filament
Resolution: 3.03 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ibn
Q-score: 0.36
Fujita J, Amesaka H, Yoshizawa T, Hibino K, Kamimura N, Kuroda N, Konishi T, Kato Y, Hara M, Inoue T, Namba K, Tanaka SI, Matsumura H
Nat Commun (2023) 14 pp. 4073-4073 [ Pubmed: 37429870 DOI: doi:10.1038/s41467-023-39807-5 ]
- Cryo-em structure of kpftsz single filament (Complex)
- Kpftsz (Complex from Klebsiella pneumoniae)
- Potassium ion (39 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Cell division protein ftsz (40 kDa, Protein from Klebsiella pneumoniae)
GroEL on hydrophilized graphene grid (high particle density)
Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T
Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]
- Groel (802 kDa, Complex from Escherichia coli)
- Groel (Protein from Escherichia coli)
SARS-CoV-2 spike protein (1-up RBD) on EG-grid
Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T
Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]
SARS-CoV-2 spike protein (1-up RBD) on Quantifoil grid
Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T
Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]
Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T
Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]
Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 7fix
Q-score: 0.651
Li J, Hamaoka N, Makino F, Kawamoto A, Lin Y, Rogner M, Nowaczyk MM, Lee YH, Namba K, Gerle C, Kurisu G
Commun Biol (2022) 5 pp. 951-951 [ DOI: doi:10.1038/s42003-022-03926-4 Pubmed: 36097054 ]
- Photosystem i 4.8k protein (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Ga-substituted ferredoxin (Complex from Thermosynechococcus elongatus BP-1)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i trimer (Complex)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Calcium ion (40 Da, Ligand)
- Ferredoxin-1 (10 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit iii (19 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Chlorophyll a (893 Da, Ligand)
- Cryo-em map of cyanobacterial photosystem i in the presence of ferredoxin and cytochrome c6 (1 MDa, Complex from Thermosynechococcus elongatus BP-1)
- Water (18 Da, Ligand)
- [2ga-2s] cluster (203 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Unknown ligand (40 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7vw6
Q-score: 0.727
Yoshikawa T, Makino F, Miyata T, Suzuki Y, Tanaka H, Namba K, Kano K, Sowa K, Kitazumi Y, Shirai O
Chem Commun (2022) 58 pp. 6478-6481 [ DOI: doi:10.1039/d2cc01541b Pubmed: 35535582 ]
- Tungsten-containing formate dehydrogenase beta subunit (62 kDa, Protein from Methylorubrum extorquens AM1)
- 2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide (740 Da, Ligand)
- Unknown atom or ion (Ligand)
- Tungsten ion (183 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Formate dehydrogenase 1 from methylorubrum extorquens am1 (170 kDa, Complex from Methylorubrum extorquens AM1)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Formate dehydrogenase (107 kDa, Protein from Methylorubrum extorquens AM1)
- Flavin mononucleotide (456 Da, Ligand)