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Stacked compact Dunaliella PSII
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pin
Q-score: 0.328
Caspy I, Fadeeva M, Mazor Y, Nelson N
eLife (2023) 12 [ Pubmed: 36799903 DOI: doi:10.7554/eLife.81150 ]
- Photosystem ii protein d1 (37 kDa, Protein from Dunaliella salina)
- Psbj (3 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Dunaliella salina)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Dunaliella salina)
- Sphingosine (299 Da, Ligand)
- (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)
- Psbw (4 kDa, Protein from Dunaliella salina)
- Bicarbonate ion (61 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Psbx (2 kDa, Protein from Dunaliella salina)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Dunaliella salina)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Cp29 (21 kDa, Protein from Dunaliella salina)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Cp26 (26 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein i (3 kDa, Protein from Dunaliella salina)
- (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)
- Chlorophyll b (907 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Dunaliella salina)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Dunaliella salina)
- 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)
- Lhcii m1 (23 kDa, Protein from Dunaliella salina)
- Ergosterol (396 Da, Ligand)
- Psbp (20 kDa, Protein from Dunaliella salina)
- Psbu (3 kDa, Protein from Dunaliella salina)
- Pheophytin a (871 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- 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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Dunaliella salina)
- Sodium ion (22 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Dunaliella salina)
- Psbm (3 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein t (3 kDa, Protein from Dunaliella salina)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Dunaliella salina)
- Psbo (25 kDa, Protein from Dunaliella salina)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Dunaliella salina)
- Dunaliella salina photosystem ii complex (Complex from Dunaliella salina)
- (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)
- Lhcii m3 (24 kDa, Protein from Dunaliella salina)
Unstacked compact Dunaliella PSII
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 7pnk
Q-score: 0.381
Caspy I, Fadeeva M, Mazor Y, Nelson N
eLife (2023) 12 [ Pubmed: 36799903 DOI: doi:10.7554/eLife.81150 ]
- Photosystem ii protein d1 (37 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Dunaliella salina)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Dunaliella salina)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Dunaliella salina)
- Sphingosine (299 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Dunaliella salina)
- (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)
- Bicarbonate ion (61 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Dunaliella salina)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Dunaliella salina)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein i (3 kDa, Protein from Dunaliella salina)
- (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)
- Chlorophyll b (907 Da, Ligand)
- Psbp (20 kDa, Protein from Green alga, Protococcus salinus)
- Psbo (25 kDa, Protein from Green alga, Protococcus salinus)
- Chloride ion (35 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Dunaliella salina)
- Digalactosyl diacyl glycerol (dgdg) (949 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)
- Psbu (3 kDa, Protein from Green alga, Protococcus salinus)
- Lhcii m1 (23 kDa, Protein from Green alga, Protococcus salinus)
- Pheophytin a (871 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Cp26 (26 kDa, Protein from Green alga, Protococcus salinus)
- 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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Dunaliella salina)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein t (3 kDa, Protein from Dunaliella salina)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein of lhcii type i, chloroplastic (24 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)
- Cytochrome b559 subunit beta (3 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Dunaliella salina)
- Dunaliella salina photosystem ii complex (Complex from Dunaliella salina)
- (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)
- Psbx (2 kDa, Protein from Green alga, Protococcus salinus)
- Psbw (4 kDa, Protein from Green alga, Protococcus salinus)
Red alga C.merolae Photosystem I
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7blz
Q-score: 0.547
Nelson N, Klaiman D, Hippler M
To Be Published
- Chlorophyll a (893 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Red alga)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Similar to chlorophyll a/b-binding protein, cp24 (19 kDa, Protein from Red alga)
- Psao (10 kDa, Protein from Red alga)
- (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)
- (1s)-2-{[{[(2r)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (751 Da, Ligand)
- Photosystem i (Complex from Cyanidioschyzon merolae strain 10D)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Red alga)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Red alga)
- Chlorophyll a isomer (893 Da, Ligand)
- Psi-k (5 kDa, Protein from Red alga)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (15 kDa, Protein from Red alga)
- Ergosterol (396 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Red alga)
- Photosystem i iron-sulfur center subunit vii (6 kDa, Protein from Red alga)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Similar to light harvesting protein (19 kDa, Protein from Red alga)
- Photosystem i iron-sulfur center (8 kDa, Protein from Red alga)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Red alga)
- Lhcr3 (19 kDa, Protein from Red alga)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Psi-f (17 kDa, Protein from Red alga)
- Phylloquinone (450 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit xii (2 kDa, Protein from Red alga)
- Phosphatidylinositol (887 Da, Ligand)
Structure of high-light grown Chlorella ohadii photosystem I
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 6zzy
Q-score: 0.561
Caspy I, Neumann E, Fadeeva M, Liveanu V, Savitsky A, Frank A, Kalisman YL, Shkolnisky Y, Murik O, Treves H, Hartmann V, Nowaczyk MM, Schuhmann W, Rogner M, Willner I, Kaplan A, Schuster G, Nelson N, Lubitz W, Nechushtai R
Nat Plants (2021) 7 pp. 1314-1322 [ Pubmed: 34462576 DOI: doi:10.1038/s41477-021-00983-1 ]
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Chlorophyll a (893 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Sphingosine (299 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- (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)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Freshwater green alga)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Freshwater green alga)
- High light grown chlorella ohadii photosystem i (1 MDa, Complex from Chlorella ohadii)
- Glutathione reductase (26 kDa, Protein from Freshwater green alga)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Oleic acid (282 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Freshwater green alga)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Freshwater green alga)
- (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 i reaction center subunit xii (3 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit vi-chloroplastic-like (10 kDa, Protein from Freshwater green alga)
- Ergosterol (396 Da, Ligand)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 2-(2-azanylethanoylamino)ethanoic acid (132 Da, Ligand)
- Psi subunit v (16 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Freshwater green alga)
- Diacyl glycerol (625 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Psi-k (8 kDa, Protein from Freshwater green alga)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- (2z,4e)-5-[(1s)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid (264 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Psi-f (18 kDa, Protein from Freshwater green alga)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Freshwater green alga)
- (3~{e},5~{e},7~{e})-6-methyl-8-[(6~{r})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one (260 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Freshwater green alga)
Structure of a minimal photosystem I from a green alga
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6rhz
Q-score: 0.467
Perez-Boerema A, Klaiman D, Caspy I, Netzer-El SY, Amunts A, Nelson N
Nat Plants (2020) 6 pp. 321-327 [ DOI: doi:10.1038/s41477-020-0611-9 Pubmed: 32123351 ]
- Photosystem i (Complex from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Green alga)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a-b binding protein, lhca2 (22 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Green alga)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Green alga)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a-b binding protein, lhca4 (23 kDa, Protein from Dunaliella salina)
- Photosystem i iron-sulfur center (8 kDa, Protein from Green alga)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Green alga)
- Photosystem i reaction center subunit iv, psae (7 kDa, Protein from Dunaliella salina)
- Photosystem i reaction center subunit iii, psaf (18 kDa, Protein from Dunaliella salina)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Phylloquinone (450 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 i reaction center subunit ii, psad (15 kDa, Protein from Dunaliella salina)