Subtomogram average of the T. pseudonana PyShell
Shimakawa G, Demulder M, Flori S, Kawamoto A, Tsuji Y, Nawaly H, Tanaka A, Tohda R, Ota T, Matsui H, Morishima N, Okubo R, Wietrzynski W, Lamm L, Righetto RD, Uwizeye C, Gallet B, Jouneau PH, Gerle C, Kurisu G, Finazzi G, Engel BD, Matsuda Y
Cell (2024) 187 pp. 5919-5934.e19 [ Pubmed: 39357521 DOI: doi:10.1016/j.cell.2024.09.013 ]
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8iwh
Q-score: 0.541
Feng Y, Li Z, Li X, Shen L, Liu X, Zhou C, Zhang J, Sang M, Han G, Yang W, Kuang T, Wang W, Shen JR
Sci Adv (2023) 9 pp. eadi8446-eadi8446 [ DOI: doi:10.1126/sciadv.adi8446 Pubmed: 37878698 ]
- Cytochrome c-550 (17 kDa, Protein from Thalassiosira pseudonana)
- Structure of psii-fcpii supercomplex containing monomeric lhcx and dimeric fcpii from thalassiosira pseudonana (Complex from Thalassiosira pseudonana)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thalassiosira pseudonana)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thalassiosira pseudonana)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii cp43 reaction center protein (51 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii protein d1 (36 kDa, Protein from Thalassiosira pseudonana)
- Fucoxanthin-chlorophyll a-c binding protein, plastid (21 kDa, Protein from Thalassiosira pseudonana)
- Bicarbonate ion (61 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Fucoxanthin chlorophyll a/c protein-li818 clade (21 kDa, Protein from Thalassiosira pseudonana)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii subunit, psbw (6 kDa, Protein from Thalassiosira pseudonana)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- Photosystem ii psb31 protein domain-containing protein (18 kDa, Protein from Thalassiosira pseudonana)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii reaction center protein i (3 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii reaction center x protein (3 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii reaction center protein j (4 kDa, Protein from Thalassiosira pseudonana)
- Fucoxanthin chlorophyll a/c protein 6 (20 kDa, Protein from Thalassiosira pseudonana)
- Chloride ion (35 Da, Ligand)
- Fucoxanthin chlorophyll a/c protein 5 (21 kDa, Protein from Thalassiosira pseudonana)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{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-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii subunit, psbq. (22 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thalassiosira pseudonana)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Ps ii complex 12 kda extrinsic protein (15 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii subunit, psbn. (2 kDa, Protein from Thalassiosira pseudonana)
- Fucoxanthin chlorophyll a/c light-harvesting protein, major type (20 kDa, Protein from Thalassiosira pseudonana)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thalassiosira pseudonana)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thalassiosira pseudonana)
- Fucoxanthin chl a/c protein, lhca clade (24 kDa, Protein from Thalassiosira pseudonana)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center m protein, plastid (12 kDa, Protein from Thalassiosira pseudonana)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thalassiosira pseudonana)
- Chlorophyll a (893 Da, Ligand)
- Oxygen-evolving enhancer protein 1 (32 kDa, Protein from Thalassiosira pseudonana)
- Cytochrome b559 subunit beta (4 kDa, Protein from Thalassiosira pseudonana)
- Ca-mn4-o5 cluster (339 Da, Ligand)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8j0d
Q-score: 0.498
Feng Y, Li Z, Li X, Shen L, Liu X, Zhou C, Zhang J, Sang M, Han G, Yang W, Kuang T, Wang W, Shen JR
Sci Adv (2023) 9 pp. eadi8446-eadi8446 [ DOI: doi:10.1126/sciadv.adi8446 Pubmed: 37878698 ]
- Chlorophyll c1 (610 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Fucoxanthin-chlorophyll a-c binding protein, plastid (17 kDa, Protein from Thalassiosira pseudonana)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Fucoxanthin chlorophyll a/c protein 6 (17 kDa, Protein from Thalassiosira pseudonana)
- Fucoxanthin chl a/c protein, lhca clade (24 kDa, Protein from Thalassiosira pseudonana)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- M1 local refinement in the psii-fcpii from the thalassiosira pseudonana at 3.19 angstrom (Complex from Thalassiosira pseudonana)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Fucoxanthin chlorophyll a/c protein 5 (18 kDa, Protein from Thalassiosira pseudonana)