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 d2 protein (38 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlorella ohadii)
- Chloroplast psby (3 kDa, Protein from Chlorella ohadii)
- Chlorophyll a b-binding cp26 (27 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein m (5 kDa, Protein from Chlorella ohadii)
- Beta-carotene (536 Da, Ligand)
- Chloroplast photosystem ii 10 kda protein (11 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chlorella ohadii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein x (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)
- (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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlorella ohadii)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chlorella ohadii)
- Chloroplast oxygen-evolving enhancer protein 1 (25 kDa, Protein from Chlorella ohadii)
- Chlorella ohadii photosystem ii (1 MDa, Complex from Chlorella ohadii)
- Photosystem ii reaction center protein i (3 kDa, Protein from Chlorella ohadii)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Chloroplast oxygen-evolving enhancer protein 3 (15 kDa, Protein from Chlorella ohadii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chlorella ohadii)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii protein d1 (37 kDa, Protein from Chlorella ohadii)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center w protein (6 kDa, Protein from Chlorella ohadii)
- Photosystem ii oxygen evolving enhancer 2 (20 kDa, Protein from Chlorella ohadii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chlorophyll a-b binding of lhcii (23 kDa, Protein from Chlorella ohadii)
- Multifunctional fusion protein (23 kDa, Protein from Chlorella ohadii)
- Chlorophyll a b binding cp29 (25 kDa, Protein from Chlorella ohadii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chlorella ohadii)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Chlorella ohadii)
- Chloride ion (35 Da, Ligand)
- Chlorophyll a-b binding of lhcii (23 kDa, Protein from Chlorella ohadii)
- Photosystem ii reaction center protein z (6 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)
Unstacked compact Dunaliella PSII
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 7pi0
Q-score: 0.623
Caspy I, Fadeeva M, Mazor Y, Nelson N
eLife (2023) 12 [ DOI: doi:10.7554/eLife.81150 Pubmed: 36799903 ]
- Photosystem ii reaction center protein k (4 kDa, Protein from Dunaliella salina)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Chlorophyll a-b binding protein of lhcii type 2, chloroplastic (23 kDa, Protein from Dunaliella salina)
- Photosystem ii d2 protein (38 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- (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)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein z (6 kDa, Protein from Dunaliella salina)
- Psii 6.1 kda protein (4 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic, cp29 (21 kDa, Protein from Dunaliella salina)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii extrinsic protein u (3 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein t (3 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem ii reaction center protein i (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)
- Photosystem ii protein d1 (37 kDa, Protein from Dunaliella salina)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Dunaliella salina)
- Oxygen-evolving enhancer protein 1, chloroplastic (25 kDa, Protein from Dunaliella salina)
- Fe (ii) ion (55 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic, cp26 (26 kDa, Protein from Dunaliella salina)
- Oxygen-evolving enhancer protein 2, chloroplastic (20 kDa, Protein from Dunaliella salina)
- Cytochrome b559 subunit beta (3 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein of lhcii type 1, chloroplastic (23 kDa, Protein from Dunaliella salina)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Dunaliella salina)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Dunaliella salina photosystem ii complex (Complex from Dunaliella salina)
- Chlorophyll a-b binding protein of lhcii type 3, chloroplastic (24 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Hypothetical protein (2 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein j (3 kDa, Protein from Dunaliella salina)
- Water (18 Da, Ligand)
- Diacyl glycerol (625 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)
- Chloride ion (35 Da, Ligand)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein h (7 kDa, Protein from Dunaliella salina)
- Sphingosine (299 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Dunaliella salina)
Unstacked stretched Dunaliella PSII
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 7pi5
Q-score: 0.542
Caspy I, Fadeeva M, Mazor Y, Nelson N
eLife (2023) 12 [ DOI: doi:10.7554/eLife.81150 Pubmed: 36799903 ]
- Photosystem ii reaction center protein k (4 kDa, Protein from Dunaliella salina)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Lhcii m3 (24 kDa, Protein from Dunaliella salina)
- Photosystem ii d2 protein (38 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- (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)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein z (6 kDa, Protein from Dunaliella salina)
- Psii 6.1 kda protein (4 kDa, Protein from Dunaliella salina)
- Glycerol (92 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein t (3 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- Cp29 (21 kDa, Protein from Dunaliella salina)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein i (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)
- Photosystem ii protein d1 (37 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Dunaliella salina)
- Cp26 (26 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Dunaliella salina)
- Pheophytin a (871 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Psbu (3 kDa, Protein from Dunaliella salina)
- Psbp (20 kDa, Protein from Dunaliella salina)
- Cytochrome b559 subunit beta (3 kDa, Protein from Dunaliella salina)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Dunaliella salina photosystem ii complex (Complex from Dunaliella salina)
- Psbo (25 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Hypothetical protein (2 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Dunaliella salina)
- Water (18 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)
- Diacyl glycerol (625 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Dunaliella salina)
- Chloride ion (35 Da, Ligand)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein h (7 kDa, Protein from Dunaliella salina)
- Sphingosine (299 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)
- Lhcii m1 (23 kDa, Protein from Dunaliella salina)
- Photosystem ii reaction center protein j (3 kDa, Protein from Dunaliella salina)
Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 7bgi
Q-score: 0.629
Caspy I, Schwartz T, Bayro-Kaiser V, Fadeeva M, Kessel A, Ben-Tal N, Nelson N
Commun Biol (2021) 4 pp. 1380- [ DOI: doi:10.1038/s42003-021-02911-7 ]
- Photosystem i reaction center subunit iv, chloroplastic (7 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (20 kDa, Protein from Chlamydomonas reinhardtii)
- Lauric acid (200 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Chlamydomonas reinhardtii)
- (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)
- Calcium ion (40 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Photosystem i of temperature sensitive chlamydomonas reinhardtii (890 kDa, Complex from Chlamydomonas reinhardtii)
- Photosystem i reaction center subunit v, chloroplastic (9 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlamydomonas reinhardtii)
- Phosphatidylinositol (887 Da, Ligand)
- Photosystem i reaction center subunit psak, chloroplastic (8 kDa, Protein from Chlamydomonas reinhardtii)
- Phylloquinone (450 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)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Octanoic acid (caprylic acid) (144 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iii, chloroplastic (17 kDa, Protein from Chlamydomonas reinhardtii)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psi subunit v (14 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chlamydomonas reinhardtii)
- Water (18 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ii, chloroplastic (16 kDa, Protein from Chlamydomonas reinhardtii)
- Sphingosine (299 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl (9e)-octadec-9-enoate (436 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Chlamydomonas reinhardtii)
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 [ Pubmed: 34462576 DOI: doi:10.1038/s41477-021-00983-1 ]
- Lhca7 (24 kDa, Protein from Chlorella ohadii)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Photosystem i subunit o (9 kDa, Protein from Chlorella ohadii)
- Beta-carotene (536 Da, Ligand)
- Photosystem i (1 MDa, Complex from Chlorella ohadii)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlorella ohadii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlorella ohadii)
- (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)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Chlorella ohadii)
- Chlorophyll b (907 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (8 kDa, Protein from Chlorella ohadii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chlorella ohadii)
- Palmitic acid (256 Da, Ligand)
- Lhca4 (23 kDa, Protein from Chlorella ohadii)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Phylloquinone (450 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)
- Psi-f (18 kDa, Protein from Chlorella ohadii)
- Oleic acid (282 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Chlorella ohadii)
- 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 Chlorella ohadii)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chlorella ohadii)
- Water (18 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chlorella ohadii)
- Astaxanthin (596 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chlorella ohadii)
- Diacyl glycerol (625 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit vi-chloroplastic-like (10 kDa, Protein from Chlorella ohadii)
- Benzene-1,3,5-triol (126 Da, Ligand)
- Sphingosine (299 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 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)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chlorella ohadii)
- Beta,beta-caroten-4-one (550 Da, Ligand)
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 ]
- Photosystem i reaction center subunit vi,photosystem i reaction center subunit vi (10 kDa, Protein from Garden pea)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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 Garden pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Psal domain-containing protein (16 kDa, Protein from Garden pea)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Garden pea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Garden pea)
- Psad (16 kDa, Protein from Garden pea)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Garden pea)
- Calcium ion (40 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Garden pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Garden pea)
- Photosystem i plastocyanin complex (650 kDa, Complex from Pisum sativum)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Garden pea)
- Plastocyanin, chloroplastic (10 kDa, Protein from Garden pea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center (10 kDa, Protein from Garden pea)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll a-b binding protein 6, chloroplastic (21 kDa, Protein from Garden pea)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Garden pea)
- Water (18 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Garden pea)
- Chlorophyll a isomer (893 Da, Ligand)
- Putative uncharacterized protein (7 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 [ Pubmed: 33020607 DOI: doi:10.1038/s41477-020-00779-9 ]
- Psae (7 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Pea)
- Pea photosystem i in complex with ferredoxin (660 kDa, Complex from Pisum sativum)
- Psal (16 kDa, Protein from Pea)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Pea)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 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)
- Psad (16 kDa, Protein from Pea)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Pea)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Lhca1 (21 kDa, Protein from Pea)
- Psag (10 kDa, Protein from Pea)
- Chlorophyll b (907 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)
- Calcium ion (40 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Pea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Pea)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Pea)
- Psah (9 kDa, Protein from Pea)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Pea)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Pea)
- Psaf (17 kDa, Protein from Pea)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Pea)
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 [ Pubmed: 33020607 DOI: doi:10.1038/s41477-020-00779-9 ]
- Psaf (17 kDa, Protein from Pisum sativum)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Psah (10 kDa, Protein from Pisum sativum)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Pisum sativum)
- Plastocyanin, chloroplastic (10 kDa, Protein from Pisum sativum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- Psag (10 kDa, Protein from Pisum sativum)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Pisum sativum)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Pisum sativum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Pisum sativum)
- Psad (16 kDa, Protein from Pisum sativum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Pisum sativum)
- Triple complex of photosystem i bound to ferredoxin and plastocyanin (660 kDa, Complex from Pisum sativum)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll b (907 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)
- Calcium ion (40 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Pisum sativum)
- Phylloquinone (450 Da, Ligand)
- Psae (7 kDa, Protein from Pisum sativum)
- Psal (16 kDa, Protein from Pisum sativum)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Pisum sativum)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Water (18 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Lhca1 (21 kDa, Protein from Pisum sativum)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Pisum sativum)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Pisum sativum)
- Chlorophyll a isomer (893 Da, Ligand)
- Psaj (4 kDa, Protein from Pisum sativum)
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 ]
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Psaf (18 kDa, Protein from Dunaliella salina)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Dunaliella salina)
- Beta-carotene (536 Da, Ligand)
- Psak (8 kDa, Protein from Dunaliella salina)
- Lhca2 (22 kDa, Protein from Dunaliella salina)
- Large dunaliella salina photosystem i-lhc supercomplex (Complex from Dunaliella salina)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- Psae (7 kDa, Protein from Dunaliella salina)
- Lhca4 (23 kDa, Protein from Dunaliella salina)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Dunaliella salina)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Dunaliella salina)
- Lhca6 (19 kDa, Protein from Dunaliella salina)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Octadecanal (268 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Dunaliella salina)
- Psad (16 kDa, Protein from Dunaliella salina)
- Calcium ion (40 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Psao (9 kDa, Protein from Dunaliella salina)
- Phylloquinone (450 Da, Ligand)
- Lhca5 (21 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Dunaliella salina)
- Psal (16 kDa, Protein from Dunaliella salina)
- Psai (4 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (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)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 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)
- Psag (10 kDa, Protein from Dunaliella salina)
- Tripalmitoylglycerol (807 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Psah (10 kDa, Protein from Dunaliella salina)
- Chlorophyll a isomer (893 Da, Ligand)