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Zhao S, Shen L, Li X, Tao Q, Li Z, Xu C, Zhou C, Yang Y, Sang M, Han G, Yu LJ, Kuang T, Shen JR, Wang W
Nat Commun (2023) 14 pp. 8164-8164 [ Pubmed: 38071196 DOI: doi:10.1038/s41467-023-44055-8 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Psbf (3 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-h1, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psba (36 kDa, Protein from Stephanocyclus meneghinianus)
- Cm-psii-fcpii (Complex from Stephanocyclus meneghinianus)
- Fcpii-j, fucoxanthin chlorophyll a/c binding protein (17 kDa, Protein from Stephanocyclus meneghinianus)
- Psbx (3 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-h2, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- Psbv (14 kDa, Protein from Stephanocyclus meneghinianus)
- Psb34 (2 kDa, Protein from Stephanocyclus meneghinianus)
- Psbb (53 kDa, Protein from Stephanocyclus meneghinianus)
- Psbe (8 kDa, Protein from Stephanocyclus meneghinianus)
- Psbh (7 kDa, Protein from Stephanocyclus meneghinianus)
- Psbd (37 kDa, Protein from Stephanocyclus meneghinianus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Psbw (5 kDa, Protein from Stephanocyclus meneghinianus)
- (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)
- 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)
- Psbq' (16 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-i, fucoxanthin chlorophyll a/c binding protein (23 kDa, Protein from Stephanocyclus meneghinianus)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Psbi (3 kDa, Protein from Stephanocyclus meneghinianus)
- Psbz (6 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-k, fucoxanthin chlorophyll a/c binding protein (13 kDa, Protein from Stephanocyclus meneghinianus)
- Chloride ion (35 Da, Ligand)
- Psbu (10 kDa, Protein from Stephanocyclus meneghinianus)
- Psbo (26 kDa, Protein from Stephanocyclus meneghinianus)
- Fcpii-g, fucoxanthin chlorophyll a/c binding protein (18 kDa, Protein from Stephanocyclus meneghinianus)
- Psbc (49 kDa, Protein from Stephanocyclus meneghinianus)
- Psbk (4 kDa, Protein from Stephanocyclus meneghinianus)
- Psbm (4 kDa, Protein from Stephanocyclus meneghinianus)
- Bicarbonate ion (61 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psby (3 kDa, Protein from Stephanocyclus meneghinianus)
- Psbl (4 kDa, Protein from Stephanocyclus meneghinianus)
- Pheophytin a (871 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Psbj (3 kDa, Protein from Stephanocyclus meneghinianus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Psbt (3 kDa, Protein from Stephanocyclus meneghinianus)
- (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)
Stacked stretched Dunaliella PSII
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7piw
Q-score: 0.236
Caspy I, Fadeeva M, Mazor Y, Nelson N
eLife (2023) 12 [ Pubmed: 36799903 DOI: doi:10.7554/eLife.81150 ]
- Photosystem ii reaction center protein j (3 kDa, Protein from Green alga, Protococcus salinus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Psbw (4 kDa, Protein from Dunaliella salina)
- Diacyl glycerol (625 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Ergosterol (396 Da, Ligand)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Dunaliella salina photosystem ii complex (Complex from Dunaliella salina)
- Cp29 (21 kDa, Protein from Dunaliella salina)
- Sodium ion (22 Da, Ligand)
- Lhcii m2 (23 kDa, Protein from Dunaliella salina)
- Lhcii m3 (24 kDa, Protein from Dunaliella salina)
- Photosystem ii protein d1 (37 kDa, Protein from Green alga, Protococcus salinus)
- Psbo (25 kDa, Protein from Dunaliella salina)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Green alga, Protococcus salinus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 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)
- Psbp (20 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein m (3 kDa, Protein from Green alga, Protococcus salinus)
- Photosystem ii reaction center protein l (4 kDa, Protein from Green alga, Protococcus salinus)
- Tripalmitoylglycerol (807 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Green alga, Protococcus salinus)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Psbu (3 kDa, Protein from Dunaliella salina)
- Glycerol (92 Da, Ligand)
- Cp29 (21 kDa, Protein from Dunaliella salina)
- Cp26 (26 kDa, Protein from Dunaliella salina)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Green alga, Protococcus salinus)
- Photosystem ii reaction center protein i (3 kDa, Protein from Green alga, Protococcus salinus)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Green alga, Protococcus salinus)
- Psbx (2 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Green alga, Protococcus salinus)
- Sphingosine (299 Da, Ligand)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Green alga, Protococcus salinus)
- Pheophytin a (871 Da, Ligand)
- Psbz (6 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lhcii m1 (23 kDa, Protein from Dunaliella salina)
- Trimethyl-[(2~{r})-1-oxidanyl-1-oxidanylidene-4-[(2~{s})-2-[(1~{s})-1-oxidanyloctadecoxy]-3-[(1~{r})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium (773 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Green alga, Protococcus salinus)
- (1~{s})-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~{s})-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)
- Cytochrome b559 subunit beta (3 kDa, Protein from Green alga, Protococcus salinus)
- Photosystem ii reaction center protein h (7 kDa, Protein from Green alga, Protococcus salinus)
- Photosystem ii reaction center protein m (3 kDa, Protein from Green alga, Protococcus salinus)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 6jlu
Q-score: 0.385
Pi X, Zhao S, Wang W, Liu D, Xu C, Han G, Kuang T, Sui SF, Shen JR
Science (2019) 365 [ Pubmed: 31371578 DOI: doi:10.1126/science.aax4406 ]
- Fcp-e (18 kDa, Protein from Chaetoceros gracilis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Psba (39 kDa, Protein from Chaetoceros gracilis)
- Psbw (5 kDa, Protein from Chaetoceros gracilis)
- Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
- (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)
- Fcp-a (18 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Psb31 (18 kDa, Protein from Chaetoceros gracilis)
- Psbc (49 kDa, Protein from Chaetoceros gracilis)
- Psbb (56 kDa, Protein from Chaetoceros gracilis)
- Psbe (9 kDa, Protein from Chaetoceros gracilis)
- 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)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psbt (3 kDa, Protein from Chaetoceros gracilis)
- Psby (3 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (22 kDa, Protein from Chaetoceros gracilis)
- Psbl (4 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 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)
- Psb34 (2 kDa, Protein from Chaetoceros gracilis)
- Psbm (4 kDa, Protein from Chaetoceros gracilis)
- Psbi (3 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- Psbf (3 kDa, Protein from Chaetoceros gracilis)
- Fcp-d (24 kDa, Protein from Chaetoceros gracilis)
- Psbd (37 kDa, Protein from Chaetoceros gracilis)
- Chloride ion (35 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Psbz (6 kDa, Protein from Chaetoceros gracilis)
- Fcp-f (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Psbk (4 kDa, Protein from Chaetoceros gracilis)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Psii-fcp supercomplex (Complex from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psbg (6 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- Psbj (3 kDa, Protein from Chaetoceros gracilis)