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)
34-fold symmetry Salmonella S ring formed by full-length FliF
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7d84
Q-score: 0.447
Kawamoto A, Miyata T, Makino F, Kinoshita M, Minamino T, Imada K, Kato T, Namba K
Nat Commun (2021) 12 pp. 4223-4223 [ DOI: doi:10.1038/s41467-021-24507-9 Pubmed: 34244518 ]
Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum)
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7cg3
Q-score: 0.264
Inoue Y, Hanazono Y, Noi K, Kawamoto A, Kimatsuka M, Harada R, Takeda K, Kita R, Iwamasa N, Shibata K, Noguchi K, Shigeta Y, Namba K, Ogura T, Miki K, Shinohara K, Yohda M
Structure (2021) 29 pp. 721-730.e6 [ Pubmed: 33651974 DOI: doi:10.1016/j.str.2021.02.002 ]
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)
Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A Resolution
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6lu1
Q-score: 0.582
Coruh O, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G
Commun Biol (2021) 4 pp. 304-304 [ Pubmed: 33686186 DOI: doi:10.1038/s42003-021-01808-9 ]
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Cyanobacterial psi monomer from t. elongatus (350 MDa, Complex from Thermosynechococcus elongatus BP-1)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Beta-carotene (536 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus elongatus BP-1)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus elongatus (strain BP-1))
- Chlorophyll a (893 Da, Ligand)
Cryo-EM structure of the human pathogen Mycoplasma pneumoniae P1
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7bwm
Q-score: 0.558
Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Perez-Luque R, Martin J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernandez-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 pp. 5188-5188 [ DOI: doi:10.1038/s41467-020-18777-y Pubmed: 33057023 ]
- Nap protein p1 (170 MDa, Cellular component from Mycoplasma pneumoniae M129)
- Adhesin p1 (143 kDa, Protein from Mycoplasma pneumoniae M129)
V1-ATPase built from cryo-EM map of V/A-ATPase from Thermus thermophilus.
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ly8
Q-score: 0.529
Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56862 Pubmed: 32639230 ]
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- Soluble domain of v/a-atpase including v1, d, two eg stalks, and n-terminal of a-subunit (500 kDa, Complex from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
The membrane-embedded Vo domain of V/A-ATPase from Thermus thermophilus
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 6ly9
Q-score: 0.417
Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56862 Pubmed: 32639230 ]
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit i (72 kDa, Protein from Thermus thermophilus HB8)
- Membrane-embedded vo domain (260 kDa, Complex from Thermus thermophilus HB8)
- V-type atp synthase subunit c (35 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit k (9 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)