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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:

Research:

perform basic research in molecular biology

Services:

offer vital services to scientists in the member states

Training

scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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primary_citation_author:"Sheng X" AND xref_links:"drugbank"

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EMD-33737

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Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri

Release date: April 26, 2023
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7yca
Q-score: 0.514

Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J

eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]

Sample:

Psag (14 kDa, Protein from Ostreococcus tauri)
Phylloquinone (450 Da, Ligand)
Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Ostreococcus tauri)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem i reaction center subunit ix (4 kDa, Protein from Ostreococcus tauri)
Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Ostreococcus tauri)
Beta-carotene (536 Da, Ligand)
Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Ostreococcus tauri)
Photosystem i psan, reaction centre subunit n (14 kDa, Protein from Ostreococcus tauri)
Photosystem i psah, reaction centre subunit vi (17 kDa, Protein from Ostreococcus tauri)
Psi subunit v (21 kDa, Protein from Ostreococcus tauri)
(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)
Lhca6 (26 kDa, Protein from Ostreococcus tauri)
Photosystem i reaction center subunit ii, chloroplastic (20 kDa, Protein from Ostreococcus tauri)
Photosystem i reaction center subunit viii (3 kDa, Protein from Ostreococcus tauri)
Chlorophyll b (907 Da, Ligand)
Chlorophyll c2 (608 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Ostreococcus tauri)
Water (18 Da, Ligand)
Photosystem i-light-harvesting complex i-prasinophyte-specific lhc protein (psi-lhci-lhcp) supercomplex (Complex from Ostreococcus tauri)
Psao (15 kDa, Protein from Ostreococcus tauri)
Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
(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 iii (24 kDa, Protein from Ostreococcus tauri)
Chlorophyll a isomer (893 Da, Ligand)
Photosystem i reaction centre subunit iv (11 kDa, Protein from Ostreococcus tauri)
Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Ostreococcus tauri)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem i reaction center subunit xii (3 kDa, Protein from Ostreococcus tauri)
(1~{s})-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-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Ostreococcus tauri)
(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-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-2-one (600 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
Lhca1 (24 kDa, Protein from Ostreococcus tauri)
Photosystem i iron-sulfur center (8 kDa, Protein from Ostreococcus tauri)
Photosystem i psag/psak protein (13 kDa, Protein from Ostreococcus tauri)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a (893 Da, Ligand)

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EMD-34733

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Cryo-EM structure of the Lhcp complex from Ostreococcus tauri

Release date: April 26, 2023
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8hg3
Q-score: 0.479

Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J

eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]

Sample:

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EMD-34735

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Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri

Release date: April 26, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8hg5
Q-score: 0.486

Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J

eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]

Sample:

[Show more]

EMD-34736

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Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri

Release date: April 26, 2023
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8hg6
Q-score: 0.412

Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J

eLife (2023) 12 [ Pubmed: 36951548 DOI: doi:10.7554/eLife.84488 ]

Sample:

[Show more]

EMD-9955

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Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii

Release date: Oct. 23, 2019
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6kac
Q-score: 0.569

Sheng X, Watanabe A, Li A, Kim E, Song C, Murata K, Song D, Minagawa J, Liu Z

Nat Plants (2019) 5 pp. 1320-1330 [ Pubmed: 31768031 DOI: doi:10.1038/s41477-019-0543-4 ]

Sample:

Chlorophyll a-b binding protein cp29 (29 kDa, Protein from Chlamydomonas reinhardtii)
Predicted protein (19 kDa, Protein from Chlamydomonas reinhardtii)
Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
Unindentified stromal protein (usp) (2 kDa, Protein from Chlamydomonas reinhardtii)
4.1 kda photosystem ii subunit (9 kDa, Protein from Chlamydomonas reinhardtii)
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)
Beta-carotene (536 Da, Ligand)
Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
Bicarbonate ion (61 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 (26 kDa, Protein from Chlamydomonas reinhardtii)
Fe (ii) ion (55 Da, Ligand)
Chlorophyll b (907 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a-b binding protein, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
Water (18 Da, Ligand)
10 kda photosystem ii polypeptide psbr (potential) (1 kDa, Protein from Chlamydomonas reinhardtii)
Chloride ion (35 Da, Ligand)
Photosystem ii reaction center protein j (4 kDa, Protein from Chlamydomonas reinhardtii)
Oxygen-evolving enhancer protein 3, chloroplastic (21 kDa, Protein from Chlamydomonas reinhardtii)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center w protein, chloroplastic (12 kDa, Protein from Chlamydomonas reinhardtii)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
(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-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
(3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
Protoporphyrin ix containing fe (616 Da, Ligand)
Oxygen-evolving enhancer protein 1, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
The c2s2-type psii-lhcii supercomplex (Complex from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a (893 Da, Ligand)
Oxygen-evolving enhancer protein 2, chloroplastic (25 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)

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EMD-9956

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Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii

Release date: Oct. 23, 2019
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6kad
Q-score: 0.447

Sheng X, Watanabe A, Li A, Kim E, Song C, Murata K, Song D, Minagawa J, Liu Z

Nat Plants (2019) 5 pp. 1320-1330 [ Pubmed: 31768031 DOI: doi:10.1038/s41477-019-0543-4 ]

Sample:

Chlorophyll a-b binding protein cp29 (29 kDa, Protein from Chlamydomonas reinhardtii)
Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
4.1 kda photosystem ii subunit (9 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Chlamydomonas reinhardtii)
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)
Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
Beta-carotene (536 Da, Ligand)
Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
Bicarbonate ion (61 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)
Fe (ii) ion (55 Da, Ligand)
Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll b (907 Da, Ligand)
The c2s2m2l2-type psii-lhcii supercomplex (Complex from Chlamydomonas reinhardtii)
Oxygen-evolving enhancer protein 1, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Chlorophyll a-b binding protein, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
Chloride ion (35 Da, Ligand)
Photosystem ii reaction center protein j (4 kDa, Protein from Chlamydomonas reinhardtii)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center w protein, chloroplastic (12 kDa, Protein from Chlamydomonas reinhardtii)
(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)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
(3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
Chlorophyll a (893 Da, Ligand)
Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
Ca-mn4-o5 cluster (339 Da, Ligand)

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EMDB [6]

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