Photosystem I reduced Plastocyanin Complex
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 6zoo
Q-score: 0.56
Caspy I, Fadeeva M, Kuhlgert S, Borovikova-Sheinker A, Klaiman D, Masrati G, Drepper F, Ben-Tal N, Hippler M, Nelson N
Biochem J (2021) 478 pp. 2371-2384 [ DOI: doi:10.1042/BCJ20210267 Pubmed: 34085703 ]
- Copper (ii) ion (63 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Garden pea)
- 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)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Garden pea)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Garden pea)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center (10 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit vi,photosystem i reaction center subunit vi (10 kDa, Protein from Garden pea)
- Psal domain-containing protein (16 kDa, Protein from Garden pea)
- Calcium ion (40 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Garden pea)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- 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 6, chloroplastic (21 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Garden pea)
- Putative uncharacterized protein (7 kDa, Protein from Garden pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Garden pea)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Garden pea)
- Plastocyanin, chloroplastic (10 kDa, Protein from Garden pea)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i plastocyanin complex (650 kDa, Complex from Pisum sativum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Garden pea)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Garden pea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Garden pea)
- Psad (16 kDa, Protein from Garden pea)
Plant PSI-ferredoxin supercomplex
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6yac
Q-score: 0.601
Caspy I, Borovikova-Sheinker A, Klaiman D, Shkolnisky Y, Nelson N
Nat Plants (2020) 6 pp. 1300-1305 [ DOI: doi:10.1038/s41477-020-00779-9 Pubmed: 33020607 ]
- Psaf (17 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Pea)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Pea)
- Phylloquinone (450 Da, Ligand)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Pea)
- Psad (16 kDa, Protein from Pea)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (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)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Pea)
- Psal (16 kDa, Protein from Pea)
- Calcium ion (40 Da, Ligand)
- Psae (7 kDa, Protein from Pea)
- (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)
- Psag (10 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Pea)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Pea)
- Psah (9 kDa, Protein from Pea)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Pea)
- Water (18 Da, Ligand)
- Lhca1 (21 kDa, Protein from Pea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Pea)
- Pea photosystem i in complex with ferredoxin (660 kDa, Complex from Pisum sativum)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Pea)
- (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 ix (4 kDa, Protein from Pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
Plant PSI-ferredoxin-plastocyanin supercomplex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6yez
Q-score: 0.536
Caspy I, Borovikova-Sheinker A, Klaiman D, Shkolnisky Y, Nelson N
Nat Plants (2020) 6 pp. 1300-1305 [ DOI: doi:10.1038/s41477-020-00779-9 Pubmed: 33020607 ]
- Psaf (17 kDa, Protein from Pea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Garden pea)
- Psad (16 kDa, Protein from Pea)
- Lhca1 (21 kDa, Protein from Pea)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psae (7 kDa, Protein from Pea)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Garden pea)
- Triple complex of photosystem i bound to ferredoxin and plastocyanin (660 kDa, Complex from Pisum sativum)
- Beta-carotene (536 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psal (16 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Garden pea)
- Calcium ion (40 Da, Ligand)
- Plastocyanin, chloroplastic (10 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Garden pea)
- (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)
- Psag (10 kDa, Protein from Pea)
- Water (18 Da, Ligand)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Garden pea)
- Psah (10 kDa, Protein from Pea)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Garden pea)
- (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 iron-sulfur center (8 kDa, Protein from Garden pea)
- Copper (ii) ion (63 Da, Ligand)
- Psaj (4 kDa, Protein from Pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Garden pea)
Dunaliella Minimal Photosystem I
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6yxr
Q-score: 0.453
Caspy I, Malavath T, Klaiman D, Fadeeva M, Shkolnisky Y, Nelson N
Biochim Biophys Acta Bioenerg (2020) 1861 pp. 148253-148253 [ DOI: doi:10.1016/j.bbabio.2020.148253 Pubmed: 32569661 ]
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psad (15 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)
- Large dunaliella salina photosystem i-lhc supercomplex (Complex from Dunaliella salina)
- Psaf (18 kDa, Protein from Dunaliella salina)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Green alga)
- Digalactosyl diacyl glycerol (dgdg) (949 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 b (907 Da, Ligand)
- Lhca4 (23 kDa, Protein from Dunaliella salina)
- Psae (7 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Green alga)
- Lhca2 (22 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Green alga)
- Chlorophyll a isomer (893 Da, Ligand)
Dunaliella Photosystem I Supercomplex
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 6sl5
Q-score: 0.53
Caspy I, Malavath T, Klaiman D, Fadeeva M, Shkolnisky Y, Nelson N
Biochim Biophys Acta Bioenerg (2020) 1861 pp. 148253-148253 [ Pubmed: 32569661 DOI: doi:10.1016/j.bbabio.2020.148253 ]
- Psah (10 kDa, Protein from Dunaliella salina)
- Phylloquinone (450 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)
- Lhca4 (23 kDa, Protein from Dunaliella salina)
- Chlorophyll a isomer (893 Da, Ligand)
- [(2~{r})-1-nonanoyloxy-3-[oxidanyl-[(2~{r},3~{s},5~{r},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{z},8~{z})-heptadeca-5,8-dienoate (722 Da, Ligand)
- Psaf (18 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Large dunaliella salina photosystem i-lhc supercomplex (Complex from Dunaliella salina)
- Lhca5 (21 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Psae (7 kDa, Protein from Dunaliella salina)
- 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)
- Beta-carotene (536 Da, Ligand)
- Psal (16 kDa, Protein from Dunaliella salina)
- Calcium ion (40 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- Psak (8 kDa, Protein from Dunaliella salina)
- Psad (16 kDa, Protein from Dunaliella salina)
- Psai (4 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 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 i reaction center subunit ix (4 kDa, Protein from Dunaliella salina)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Lhca2 (22 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Dunaliella salina)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Dunaliella salina)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Dunaliella salina)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Dunaliella salina)
- Lhca6 (19 kDa, Protein 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)
- Psao (9 kDa, Protein from Dunaliella salina)
- Octadecanal (268 Da, Ligand)
- Psag (10 kDa, Protein from Dunaliella salina)
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 ]
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i (Complex from Dunaliella salina)
- Photosystem i iron-sulfur center (8 kDa, Protein from Green alga)
- Chlorophyll a-b binding protein, lhca4 (23 kDa, Protein from Dunaliella salina)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Green alga)
- Photosystem i reaction center subunit ii, psad (15 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Green alga)
- Digalactosyl diacyl glycerol (dgdg) (949 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 b (907 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Green alga)
- Chlorophyll a-b binding protein, lhca2 (22 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iii, psaf (18 kDa, Protein from Dunaliella salina)
- Photosystem i reaction center subunit iv, psae (7 kDa, Protein from Dunaliella salina)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Green alga)
- Chlorophyll a isomer (893 Da, Ligand)