Kawamoto A, Vizarraga D, Marcos-Silva M, Martin J, Makino F, Miyata T, Roel J, Marcos E, Aparicio D, Fita I, Miyata M, Pinol J, Namba K, Kenri T
bioRxiv (2023) [ DOI: doi:10.1101/2023.07.31.551205 ]
Cryo-EM structure of the barley Yellow stripe 1 transporter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7wsr
Q-score: 0.533
Yamagata A, Murata Y, Namba K, Terada T, Fukai S, Shirouzu M
Nat Commun (2022) 13 pp. 7180-7180 [ Pubmed: 36424382 DOI: doi:10.1038/s41467-022-34930-1 ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Yellow stripe 1 in the apo state (Cell from Hordeum vulgare)
- Iron-phytosiderophore transporter (76 kDa, Protein from Hordeum vulgare)
Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-DMA
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7wst
Q-score: 0.596
Yamagata A, Murata Y, Namba K, Terada T, Fukai S, Shirouzu M
Nat Commun (2022) 13 pp. 7180-7180 [ Pubmed: 36424382 DOI: doi:10.1038/s41467-022-34930-1 ]
- (2~{s})-1-[(3~{s})-3-[[(3~{s})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]azetidine-2-carboxylic acid (304 Da, Ligand)
- Iron-phytosiderophore transporter (76 kDa, Protein from Hordeum vulgare)
- Yellow stripe 1 in the apo state (Cell from Hordeum vulgare)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-PDMA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7wsu
Q-score: 0.561
Yamagata A, Murata Y, Namba K, Terada T, Fukai S, Shirouzu M
Nat Commun (2022) 13 pp. 7180-7180 [ Pubmed: 36424382 DOI: doi:10.1038/s41467-022-34930-1 ]
- Iron-phytosiderophore transporter (76 kDa, Protein from Hordeum vulgare)
- (2~{s})-1-[(3~{s})-3-[[(3~{s})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]pyrrolidine-2-carboxylic acid (318 Da, Ligand)
- Yellow stripe 1 in the apo state (Cell from Hordeum vulgare)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
Cryo-EM structure of cyanobacterial PSI in presence of Gallium-substituted ferredoxin (GaFd)
Li J, Hamaoka N, Makino F, Kawamoto A, Lin Y, Rögner M, Nowaczyk MM, Lee YH, Namba K, Gerle C, Kurisu G
Commun Biol (2022) 5 [ DOI: 10.1038/s42003-022-03926-4 Pubmed: 36097054 ]
Image sets:
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 [ Pubmed: 36097054 DOI: doi:10.1038/s42003-022-03926-4 ]
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Ferredoxin-1 (10 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 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)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Water (18 Da, Ligand)
- Ga-substituted ferredoxin (Complex from Thermosynechococcus elongatus BP-1)
- Photosystem i trimer (Complex)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Calcium ion (40 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iii (19 kDa, Protein from Thermosynechococcus vestitus BP-1)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vestitus BP-1)
- [2ga-2s] cluster (203 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Unknown ligand (40 Da, Ligand)
- Photosystem i 4.8k protein (4 kDa, Protein from Thermosynechococcus vestitus BP-1)
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 7vq0
Q-score: 0.415
Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A
Commun Biol (2022) 5 pp. 669-669 [ DOI: doi:10.1038/s42003-022-03630-3 Pubmed: 35794202 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Neutralizing nanobody p86 (13 kDa, Protein from Vicugna pacos)
- Sars-cov-2 spike protein (2-up rbd) bound to neutralizing nanobodies p86 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (2-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobodies p86 (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of the SARS-CoV-2 spike protein (3-up RBD) bound to neutralizing nanobodies P86
Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A
Commun Biol (2022) 5 pp. 669-669 [ DOI: doi:10.1038/s42003-022-03630-3 Pubmed: 35794202 ]
- Neutralizing nanobody p86 (Protein from Vicugna pacos)
- Sars-cov-2 spike protein (3-up rbd) bound to neutralizing nanobodies p86 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (3-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobody p86 (Complex)
- Spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of the SARS-CoV-2 spike protein (1-up RBD) bound to neutralizing nanobodies P17
Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A
Commun Biol (2022) 5 pp. 669-669 [ DOI: doi:10.1038/s42003-022-03630-3 Pubmed: 35794202 ]
- Neutralizing nanobodies p17 (Complex)
- Sars-cov-2 spike protein (1-up rbd) bound to neutralizing nanobodies p17 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (1-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobody p17 (Protein from Vicugna pacos)
- Spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)