Kawamoto A, Vizarraga D, Marcos-Silva M, Martin J, Makino F, Miyata T, Roel J, Marcos E, Aparicio D, Fita I, Miyata M, Pinyol J, Namba K, Kenri T
To Be Published
- Water (18 Da, Ligand)
- Anti-adhesive fab fragment (Complex from Mus musculus)
- Adhesin p1 (158 kDa, Protein from Mycoplasmoides pneumoniae M129)
- Heavy chain fab (23 kDa, Protein from Mus musculus)
- Mycoplasma pneumoniae adhesin p1 complexed with the anti-adhesive fab fragment. (200 kDa, Complex)
- Light chain fab (24 kDa, Protein from Mus musculus)
- Adhesin p1 (Complex from Mycoplasmoides pneumoniae M129)
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 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 [ 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 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 ]
- Neutralizing nanobody p86 (13 kDa, Protein from Vicugna pacos)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (2-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobodies p86 (Complex)
- Sars-cov-2 spike protein (2-up rbd) bound to neutralizing nanobodies p86 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 ]
- Spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (3-up rbd) bound to neutralizing nanobodies p86 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Neutralizing nanobody p86 (Complex)
- Neutralizing nanobody p86 (Protein from Vicugna pacos)
- Sars-cov-2 spike protein (3-up rbd) (Complex from Vicugna pacos)
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 ]
- Sars-cov-2 spike protein (1-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobody p17 (Protein from Vicugna pacos)
- Sars-cov-2 spike protein (1-up rbd) bound to neutralizing nanobodies p17 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Neutralizing nanobodies p17 (Complex)
- Spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of the SARS-CoV-2 spike protein (2-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 ]
- Sars-cov-2 spike protein (2-up rbd) (Complex from Vicugna pacos)
- Neutralizing nanobody p17 (Protein from Vicugna pacos)
- Neutralizing nanobodies p17 (Complex)
- Spike glycoprotein (Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike protein (2-up rbd) bound to neutralizing nanobodies p17 (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of a membrane protein
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6lbh
Q-score: 0.461
Jin F, Sun M, Fujii T, Yamada Y, Wang J, Maturana AD, Wada M, Su S, Ma J, Takeda H, Kusakizako T, Tomita A, Nakada-Nakura Y, Liu K, Uemura T, Nomura Y, Nomura N, Ito K, Nureki O, Namba K, Iwata S, Yu Y, Hattori M
PLoS Biol (2021) 19 pp. e3001231-e3001231 [ DOI: doi:10.1371/journal.pbio.3001231 Pubmed: 33905418 ]
- Fab heavy chain (24 kDa, Protein from Mus musculus)
- Magnesium transporter mgte (19 kDa, Protein from Thermus thermophilus HB8)
- Mgte-fab complex (Complex from Thermus thermophilus)
- Fab light chain (23 kDa, Protein from Mus musculus)
Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Pérez-Luque R, Martín J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernández-Huerta M, Scheffer MP, Pinyol J, Frangakis AS, Lluch-Senar M, Mori S, Shibayama K, Kenri T, Kato T, Namba K, Fita I, Miyata M, Aparicio D
Nat Commun (2020) 11 [ Pubmed: 33057023 DOI: 10.1038/s41467-020-18777-y ]
Image sets: