Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8bd3
Q-score: 0.574
Fadeeva M, Klaiman D, Caspy I, Nelson N
Cells (2023) 12 [ DOI: doi:10.3390/cells12151971 Pubmed: 37566050 ]
- Photosystem ii reaction center protein m (5 kDa, Protein from Chlorella ohadii)
- (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)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chlorella ohadii)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chlorella ohadii)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chlorella ohadii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Multifunctional fusion protein (23 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein x (3 kDa, Protein from Chlorella ohadii)
- Chloroplast photosystem ii 10 kda protein (11 kDa, Protein from Chlorella ohadii)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlorella ohadii)
- Chlorophyll a b binding cp29 (25 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlorella ohadii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlorella ohadii)
- Chlorella ohadii photosystem ii (1 MDa, Complex from Chlorella ohadii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlorella ohadii)
- Chlorophyll a b-binding cp26 (27 kDa, Protein from Chlorella ohadii)
- 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)
- Photosystem ii d2 protein (38 kDa, Protein from Chlorella ohadii)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Chlorophyll b (907 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)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Photosystem ii protein d1 (37 kDa, Protein from Chlorella ohadii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlorella ohadii)
- Chloroplast oxygen-evolving enhancer protein 1 (25 kDa, Protein from Chlorella ohadii)
- Chloride ion (35 Da, Ligand)
- Chlorophyll a-b binding of lhcii (23 kDa, Protein from Chlorella ohadii)
- Photosystem ii oxygen evolving enhancer 2 (20 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein i (3 kDa, Protein from Chlorella ohadii)
- Pheophytin a (871 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Water (18 Da, Ligand)
- Chloroplast psby (3 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center w protein (6 kDa, Protein from Chlorella ohadii)
- Chloroplast oxygen-evolving enhancer protein 3 (15 kDa, Protein from Chlorella ohadii)
- Chlorophyll a-b binding of lhcii (23 kDa, Protein from Chlorella ohadii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Structure of low-light grown Chlorella ohadii Photosystem I
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6zzx
Q-score: 0.621
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 [ DOI: doi:10.1038/s41477-021-00983-1 Pubmed: 34462576 ]
- (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)
- Tripalmitoylglycerol (807 Da, Ligand)
- Photosystem i reaction center subunit vi-chloroplastic-like (10 kDa, Protein from Freshwater green alga)
- Photosystem i subunit o (9 kDa, Protein from Freshwater green alga)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Freshwater green alga)
- Phosphatidylethanolamine (734 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Glutathione reductase (26 kDa, Protein from Freshwater green alga)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Palmitic acid (256 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)
- Photosystem i reaction center subunit chloroplastic (8 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Freshwater green alga)
- Astaxanthin (596 Da, Ligand)
- Oleic acid (282 Da, Ligand)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Lhca4 (23 kDa, Protein from Freshwater green alga)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Freshwater green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Chlorophyll b (907 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 viii (3 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Freshwater green alga)
- Lhca7 (24 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Freshwater green alga)
- Photosystem i (1 MDa, Complex from Chlorella ohadii)
- Chlorophyll a (893 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Water (18 Da, Ligand)
- Benzene-1,3,5-triol (126 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psi-f (18 kDa, Protein from Freshwater green alga)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Sphingosine (299 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- (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)
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 ]
- Psi-f (18 kDa, Protein from Freshwater green alga)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Psi subunit v (16 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Freshwater green alga)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Freshwater green alga)
- High light grown chlorella ohadii photosystem i (1 MDa, Complex from Chlorella ohadii)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Freshwater green alga)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Freshwater green alga)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit vi-chloroplastic-like (10 kDa, Protein from Freshwater green alga)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psi-k (8 kDa, Protein from Freshwater green alga)
- Beta-carotene (536 Da, Ligand)
- Glutathione reductase (26 kDa, Protein from Freshwater green alga)
- 2-(2-azanylethanoylamino)ethanoic acid (132 Da, Ligand)
- Palmitic acid (256 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)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Sphingosine (299 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 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)
- Photosystem i iron-sulfur center (8 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Oleic acid (282 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Freshwater green alga)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Freshwater green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 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)
- (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)
- Ergosterol (396 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Structure of small high-light grown Chlorella ohadii photosystem I
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7a4p
Q-score: 0.278
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 Chlorella ohadii)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Small high light grown chlorella ohadii photosystem i (900 kDa, Complex from Chlorella ohadii)
- Photosystem i reaction center subunit vi-chloroplastic-like (329 Da, Protein from Chlorella ohadii)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chlorella ohadii)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Chlorella ohadii)
- Chlorophyll b (907 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psi-f (18 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chlorella ohadii)
- Psi-k (8 kDa, Protein from Chlorella ohadii)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chlorella ohadii)
- Glutathione reductase (26 kDa, Protein from Chlorella ohadii)
- 2-(2-azanylethanoylamino)ethanoic acid (132 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Sphingosine (299 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chlorella ohadii)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chlorella ohadii)
- (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 (25 kDa, Protein from Chlorella ohadii)
- Oleic acid (282 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Chlorella ohadii)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlorella ohadii)
- Psi subunit v (16 kDa, Protein from Chlorella ohadii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 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 p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chlorella ohadii)
- (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)
- Ergosterol (396 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Chlorella ohadii)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)