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EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

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perform basic research in molecular biology

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offer vital services to scientists in the member states

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represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

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Structural biology

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Structural biology

Heidelberg

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Hinxton

EMBL-EBI: European Bioinformatics Institute

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Epigenetics and neurobiology

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author:"Li X" AND xref_links:"chebi" AND author_name:"Yang" AND author_name:"Xy"

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EMD-37414

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Structure of PSII-ACPII supercomplex from cryptophyte algae

Release date: June 5, 2024
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 8wb4
Q-score: 0.539

Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G

Nat Commun (2024) 15 pp. 4535-4535 [ DOI: doi:10.1038/s41467-024-48878-x Pubmed: 38806516 ]

Sample:

Chlorophyll c2 (608 Da, Ligand)
Photosystem ii reaction center protein l (4 kDa, Protein from Chroomonas placoidea)
Photosystem ii d2 protein (39 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center x protein (4 kDa, Protein from Chroomonas placoidea)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein k (5 kDa, Protein from Chroomonas placoidea)
Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii reaction center protein r (2 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein i (4 kDa, Protein from Chroomonas placoidea)
(6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein j (3 kDa, Protein from Chroomonas placoidea)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center protein t (3 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center protein u (15 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein q (1 kDa, Protein from Chroomonas placoidea)
Photosystem ii protein d1 (39 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chroomonas placoidea)
Fe (ii) ion (55 Da, Ligand)
Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chroomonas placoidea)
Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein z (6 kDa, Protein from Chroomonas placoidea)
Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein w (11 kDa, Protein from Chroomonas placoidea)
Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein o (34 kDa, Protein from Chroomonas placoidea)
Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Photosystem ii cytochrome c550 (17 kDa, Protein from Chroomonas placoidea)
Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
Structure of psii-acpii supercomplex from cryptophyte algae (Complex from Chroomonas placoidea)
Photosystem ii reaction center m (11 kDa, Protein from Chroomonas placoidea)
Photosystem ii reaction center protein h (7 kDa, Protein from Chroomonas placoidea)
Cytochrome b559 subunit beta (4 kDa, Protein from Chroomonas placoidea)
Chloride ion (35 Da, Ligand)
Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chroomonas placoidea)
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)
Acpii-2 (23 kDa, Protein from Chroomonas placoidea)

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EMD-38419

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Structure of ACPII-CCPII from cryptophyte algae

Release date: June 5, 2024
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8xkl
Q-score: 0.49

Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G

Nat Commun (2024) 15 pp. 4535-4535 [ DOI: doi:10.1038/s41467-024-48878-x Pubmed: 38806516 ]

Sample:

Chlorophyll a (893 Da, Ligand)
Chlorophyll c2 (608 Da, Ligand)
Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
(1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
(6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
Structure of acpii-ccpii from cryptophyte algae (Complex from Chroomonas placoidea)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
Acpii-2 (23 kDa, Protein from Chroomonas placoidea)

[Show more]

EMD-36678

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PSI-AcpPCI supercomplex from Amphidinium carterae

Release date: Feb. 28, 2024
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8jw0
Q-score: 0.51

Li X, Li Z, Wang F, Zhao S, Xu C, Mao Z, Duan J, Feng Y, Yang Y, Shen L, Wang G, Yang Y, Yu LJ, Sang M, Han G, Wang X, Kuang T, Shen JR, Wang W

PNAS (2024) 121 pp. e2315476121-e2315476121 [ Pubmed: 38319970 DOI: doi:10.1073/pnas.2315476121 ]

Sample:

Peridinin (630 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-11, acppci-11 (19 kDa, Protein from Amphidinium carterae)
Beta-carotene (536 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-14, acppci-14 (17 kDa, Protein from Amphidinium carterae)
Photosystem i psab (67 kDa, Protein from Amphidinium carterae)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
(3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-15, acppci-15 (17 kDa, Protein from Amphidinium carterae)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem i psaj (7 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-5, acppci-5 (20 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-9, acppci-9 (17 kDa, Protein from Amphidinium carterae)
Photosystem i psaf (20 kDa, Protein from Amphidinium carterae)
Psi-acppci supercomplex from amphidinium carterae (Complex from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-12, acppci-12 (17 kDa, Protein from Amphidinium carterae)
Photosystem i psai (14 kDa, Protein from Amphidinium carterae)
Photosystem i psar (14 kDa, Protein from Amphidinium carterae)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-6, acppci-6 (19 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-10, acppci-10 (19 kDa, Protein from Amphidinium carterae)
Photosystem i psam (9 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-7, acppci-7 (21 kDa, Protein from Amphidinium carterae)
Photosystem i psaa (70 kDa, Protein from Amphidinium carterae)
Photosystem i psad (28 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-8, acppci-8 (23 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-2, acppci-2 (19 kDa, Protein from Amphidinium carterae)
Photosystem i psae (8 kDa, Protein from Amphidinium carterae)
Photosystem i psac (9 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-13, acppci-13 (17 kDa, Protein from Amphidinium carterae)
Phylloquinone (450 Da, Ligand)
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-chlorophyll c-peridinin-protein-complex i-3, acppci-3 (18 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-4, acppci-4 (18 kDa, Protein from Amphidinium carterae)
Photosystem i psal (27 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-16, acppci-16 (17 kDa, Protein from Amphidinium carterae)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-1, acppci-1 (15 kDa, Protein from Amphidinium carterae)
Iron/sulfur cluster (351 Da, Ligand)
[(1~{s},5~{r})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{s},4~{s},6~{r})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate (642 Da, Ligand)
Chlorophyll c1 (610 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-17, acppci-17 (17 kDa, Protein from Amphidinium carterae)

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EMD-36742

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PSI-AcpPCI supercomplex from Symbiodinium

Release date: Feb. 28, 2024
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8jze
Q-score: 0.518

Li X, Li Z, Wang F, Zhao S, Xu C, Mao Z, Duan J, Feng Y, Yang Y, Shen L, Wang G, Yang Y, Yu LJ, Sang M, Han G, Wang X, Kuang T, Shen JR, Wang W

PNAS (2024) 121 pp. e2315476121-e2315476121 [ Pubmed: 38319970 DOI: doi:10.1073/pnas.2315476121 ]

Sample:

Peridinin (630 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-8, acppci-8 (24 kDa, Protein from Symbiodinium)
Photosystem i unk (11 kDa, Protein from Symbiodinium)
Beta-carotene (536 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-4, acppci-4 (19 kDa, Protein from Symbiodinium)
(3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-6, acppci-6 (19 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-12, acppci-12 (17 kDa, Protein from Symbiodinium)
Photosystem i unk (6 kDa, Protein from Symbiodinium)
Photosystem i psai (13 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-2, acppci-2 (19 kDa, Protein from Symbiodinium)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-7, acppci-7 (21 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-15, acppci-15 (17 kDa, Protein from Symbiodinium)
Photosystem i psad (24 kDa, Protein from Symbiodinium)
Photosystem i psal (27 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-3, acppci-3 (22 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-10, acppci-10 (20 kDa, Protein from Symbiodinium)
Photosystem i psae (8 kDa, Protein from Symbiodinium)
Phylloquinone (450 Da, Ligand)
Photosystem i psaa (75 kDa, Protein from Symbiodinium)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Psi-acppci supercomplex from symbiodinium (Complex from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-13, acppci-13 (17 kDa, Protein from Symbiodinium)
Photosystem i psar (15 kDa, Protein from Symbiodinium)
Chlorophyll a (893 Da, Ligand)
Photosystem i psaf (20 kDa, Protein from Symbiodinium)
Photosystem i psaj (11 kDa, Protein from Symbiodinium)
[(1~{s},5~{r})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{s},4~{s},6~{r})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate (642 Da, Ligand)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-11, acppci-11 (21 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-14, acppci-14 (17 kDa, Protein from Symbiodinium)
Chlorophyll c1 (610 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-9, acppci-9 (17 kDa, Protein from Symbiodinium)
Photosystem i psab (74 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-5, acppci-5 (20 kDa, Protein from Symbiodinium)
Photosystem i psac (9 kDa, Protein from Symbiodinium)
Photosystem i psam (8 kDa, Protein from Symbiodinium)

[Show more]

EMD-36743

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PSI-AcpPCI supercomplex from Symbiodinium

Release date: Feb. 28, 2024
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8jzf
Q-score: 0.537

Li X, Li Z, Wang F, Zhao S, Xu C, Mao Z, Duan J, Feng Y, Yang Y, Shen L, Wang G, Yang Y, Yu LJ, Sang M, Han G, Wang X, Kuang T, Shen JR, Wang W

PNAS (2024) 121 pp. e2315476121-e2315476121 [ Pubmed: 38319970 DOI: doi:10.1073/pnas.2315476121 ]

Sample:

Peridinin (630 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-8, acppci-8 (24 kDa, Protein from Symbiodinium)
Photosystem i unk (11 kDa, Protein from Symbiodinium)
Beta-carotene (536 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-4, acppci-4 (19 kDa, Protein from Symbiodinium)
(3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-6, acppci-6 (19 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-12, acppci-12 (17 kDa, Protein from Symbiodinium)
Photosystem i unk (6 kDa, Protein from Symbiodinium)
Photosystem i psai (13 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-2, acppci-2 (19 kDa, Protein from Symbiodinium)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-7, acppci-7 (21 kDa, Protein from Symbiodinium)
Photosystem i psad (24 kDa, Protein from Symbiodinium)
Photosystem i psal (27 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-3, acppci-3 (22 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-10, acppci-10 (20 kDa, Protein from Symbiodinium)
Photosystem i psae (8 kDa, Protein from Symbiodinium)
Phylloquinone (450 Da, Ligand)
Photosystem i psaa (75 kDa, Protein from Symbiodinium)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Psi-acppci supercomplex from symbiodinium (Complex from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-13, acppci-13 (17 kDa, Protein from Symbiodinium)
Photosystem i psar (15 kDa, Protein from Symbiodinium)
Chlorophyll a (893 Da, Ligand)
Photosystem i psaf (20 kDa, Protein from Symbiodinium)
Photosystem i psaj (11 kDa, Protein from Symbiodinium)
[(1~{s},5~{r})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{s},4~{s},6~{r})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate (642 Da, Ligand)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-11, acppci-11 (21 kDa, Protein from Symbiodinium)
Chlorophyll c1 (610 Da, Ligand)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-9, acppci-9 (17 kDa, Protein from Symbiodinium)
Photosystem i psab (74 kDa, Protein from Symbiodinium)
Chlorophyll a-chlorophyll c-peridinin-protein-complex i-5, acppci-5 (20 kDa, Protein from Symbiodinium)
Photosystem i psac (9 kDa, Protein from Symbiodinium)
Photosystem i psam (8 kDa, Protein from Symbiodinium)

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