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