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PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Resolution: 1.92 Å
EM Method: Single-particle
Fitted PDBs: 8wey
Q-score: 0.662
Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, Nagao R
PNAS (2024) 121 pp. e2319658121-e2319658121 [ Pubmed: 38442179 DOI: doi:10.1073/pnas.2319658121 ]
- Water (18 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psi-lhci (550 kDa, Complex from Cyanidium caldarium)
- Lhcr1 (24 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanidium caldarium)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{r} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol (568 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanidium caldarium)
- Lhcr2 (24 kDa, Protein from Cyanidium caldarium)
- Phylloquinone (450 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanidium caldarium)
- Beta-carotene (536 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit x (7 kDa, Protein from Cyanidium caldarium)
- Photosystem i subunit o (16 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a isomer (893 Da, Ligand)
- Unknown ligand (Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanidium caldarium)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanidium caldarium)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanidium caldarium)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanidium caldarium)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Cyanidium caldarium)
- Lhcr3 (23 kDa, Protein from Cyanidium caldarium)
RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ Pubmed: 36423304 DOI: 10.1126/science.add7347 ]
Image sets:
Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex
Kato K, Zhou W, Okazaki S, Isayama Y, Nishizawa T, Gootenberg JS, Abudayyeh OO, Nishimasu H
Cell (2022) 185 pp. 2324-2337.e16 [ Pubmed: 35643083 DOI: 10.1016/j.cell.2022.05.003 ]
Image sets:
Human ATAD2 Walker B mutant, ATP state
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8h3h
Q-score: 0.571
Cho C, Ganser C, Uchihashi T, Kato K, Song JJ
Commun Biol (2023) 6 pp. 993-993 [ DOI: doi:10.1038/s42003-023-05373-1 Pubmed: 37770645 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atad2 (Complex from Homo sapiens)
- Atpase family aaa domain-containing protein 2 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Human ATAD2 Walker B mutant-H3/H4K5Q complex, ATP state
Resolution: 3.79 Å
EM Method: Single-particle
Fitted PDBs: 8juw
Q-score: 0.364
Cho C, Ganser C, Uchihashi T, Kato K, Song JJ
Commun Biol (2023) 6 pp. 993-993 [ DOI: doi:10.1038/s42003-023-05373-1 Pubmed: 37770645 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atad2 (Complex from Homo sapiens)
- Atpase family aaa domain-containing protein 2 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Human ATAD2 Walker B mutant-H3/H4K5Q complex, ATP state (Class II)
Resolution: 4.34 Å
EM Method: Single-particle
Fitted PDBs: 8juy
Q-score: 0.239
Cho C, Ganser C, Uchihashi T, Kato K, Song JJ
Commun Biol (2023) 6 pp. 993-993 [ DOI: doi:10.1038/s42003-023-05373-1 Pubmed: 37770645 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atad2 (Complex from Homo sapiens)
- Atpase family aaa domain-containing protein 2 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Human ATAD2 Walker B mutant-H3/H4K5Q complex, ATP state (Class III)
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 8juz
Q-score: 0.18
Cho C, Ganser C, Uchihashi T, Kato K, Song JJ
Commun Biol (2023) 6 pp. 993-993 [ DOI: doi:10.1038/s42003-023-05373-1 Pubmed: 37770645 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atad2 (Complex from Homo sapiens)
- Atpase family aaa domain-containing protein 2 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8f2r
Q-score: 0.381
Healy MD, McNally KE, Butkovic R, Chilton M, Kato K, Sacharz J, McConville C, Moody ERR, Shaw S, Planelles-Herrero VJ, Yadav SKN, Ross J, Borucu U, Palmer CS, Chen KE, Croll TI, Hall RJ, Caruana NJ, Ghai R, Nguyen THD, Heesom KJ, Saitoh S, Berger I, Schaffitzel C, Williams TA, Stroud DA, Derivery E, Collins BM, Cullen PJ
Cell (2023) 186 pp. 2219-2237.e29 [ Pubmed: 37172566 DOI: doi:10.1016/j.cell.2023.04.003 ]
- Comm domain-containing protein 7 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 5 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 4 (21 kDa, Protein from Homo sapiens)
- Human ccc complex (Complex from Homo sapiens)
- Comm domain-containing protein 2 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 8 (20 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 3 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 1 (20 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 9 (21 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 10 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 6 (8 kDa, Protein from Homo sapiens)
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 8f2u
Q-score: 0.408
Healy MD, McNally KE, Butkovic R, Chilton M, Kato K, Sacharz J, McConville C, Moody ERR, Shaw S, Planelles-Herrero VJ, Yadav SKN, Ross J, Borucu U, Palmer CS, Chen KE, Croll TI, Hall RJ, Caruana NJ, Ghai R, Nguyen THD, Heesom KJ, Saitoh S, Berger I, Schaffitzel C, Williams TA, Stroud DA, Derivery E, Collins BM, Cullen PJ
Cell (2023) 186 pp. 2219-2237.e29 [ Pubmed: 37172566 DOI: doi:10.1016/j.cell.2023.04.003 ]
- Comm domain-containing protein 7 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 8 (21 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 4 (21 kDa, Protein from Homo sapiens)
- Human ccc complex (Complex from Homo sapiens)
- Comm domain-containing protein 2 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 1 (21 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 3 (22 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 5 (28 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 10 (24 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 6 (9 kDa, Protein from Homo sapiens)
- Comm domain-containing protein 9 (21 kDa, Protein from Homo sapiens)
- Coiled-coil domain-containing protein 93 (73 kDa, Protein from Homo sapiens)
- Coiled-coil domain-containing protein 22 (70 kDa, Protein from Homo sapiens)
Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8h3m
Q-score: 0.635
Ishimaru H, Nishimura M, Tjan LH, Sutandhio S, Marini MI, Effendi GB, Shigematsu H, Kato K, Hasegawa N, Aoki K, Kurahashi Y, Furukawa K, Shinohara M, Nakamura T, Arii J, Nagano T, Nakamura S, Sano S, Iwata S, Okamura S, Mori Y
J Virol (2023) 97 pp. e0028623-e0028623 [ Pubmed: 37191569 DOI: doi:10.1128/jvi.00286-23 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Mo1 heavy chain (48 kDa, Protein from Homo sapiens)
- Spike protein complexed with mo1 fab (500 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)