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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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Barcelona

Tissue biology and disease modelling

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Structural biology

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Structural biology

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EMBL-EBI: European Bioinformatics Institute

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Epigenetics and neurobiology

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sample_name:"R2" AND citation_journal_name:"J INTEGR PLANT BIOL" AND author_name:"J"

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EMD-39177

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Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

Release date: Feb. 19, 2025
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8ydm
Q-score: 0.491

Huang G, Dong S, Ma L, Li L, Ju J, Wang MJ, Zhang JP, Sui SF, Qin X

J Integr Plant Biol (2025) [ DOI: doi:10.1111/jipb.13853 Pubmed: 39912559 ]

Sample:

Hypothetical protein chain n (6 kDa, Protein from Chloroflexus aurantiacus J-10-fl)
Manganese (ii) ion (54 Da, Ligand)
Gamma-carotene (536 Da, Ligand)
Cryo-em structure of carc-lh complex from chloroflexus aurantiacus (Complex from Chloroflexus aurantiacus J-10-fl)
Reaction center protein m chain (34 kDa, Protein from Chloroflexus aurantiacus J-10-fl)
Bacteriochlorophyll a (911 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
Light-harvesting protein b-808/866 beta chain (6 kDa, Protein from Chloroflexus aurantiacus J-10-fl)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
Cytochrome c-554 (45 kDa, Protein from Chloroflexus aurantiacus J-10-fl)
Light-harvesting protein b-808/866 alpha chain (6 kDa, Protein from Chloroflexus aurantiacus J-10-fl)
Reaction center protein l chain (35 kDa, Protein from Chloroflexus aurantiacus J-10-fl)

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EMD-60032

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PSI-FCPI-L in Thalassiosira pseudonana

Release date: Dec. 25, 2024
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8zeh
Q-score: 0.566

Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W

J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]

Sample:

Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Beta-carotene (536 Da, Ligand)
Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
(3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
(1~{r})-3,5,5-trimethyl-4-[(1~{e},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-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Tp-lhcr18 (16 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chlorophyll a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Phylloquinone (450 Da, Ligand)
Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
(3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll c1 (610 Da, Ligand)
Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)

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EMD-60044

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Tp-PSI-FCPI-S in Thalassiosira pseudonana

Release date: Dec. 25, 2024
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8zet
Q-score: 0.485

Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W

J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]

Sample:

Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Beta-carotene (536 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
(1~{r})-3,5,5-trimethyl-4-[(1~{e},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-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
(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-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Phylloquinone (450 Da, Ligand)
Tp-psi-fcpi-s (Complex from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
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 i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Iron/sulfur cluster (351 Da, Ligand)
(3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
Chlorophyll c1 (610 Da, Ligand)
Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)

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EMD-36907

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Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris

Release date: May 22, 2024
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8k5o

Qi CH, Wang GL, Wang FF, Wang J, Wang XP, Zou MJ, Ma F, Madigan MT, Kimura Y, Wang-Otomo ZY, Yu LJ

J Integr Plant Biol (2024) 66 pp. 2262-2272 [ DOI: doi:10.1111/jipb.13628 Pubmed: 38411333 ]

Sample:

Light-harvesting lhi (7 kDa, Protein from Halorhodospira halochloris)
Cardiolipin (1 kDa, Ligand)
Trans-geranyl bacteriochlorophyll b (907 Da, Ligand)
Rc-lh core complex (Complex from Halorhodospira halochloris)
Photosynthetic reaction center h subunit (31 kDa, Protein from Halorhodospira halochloris)
Antenna complex alpha/beta subunit domain-containing protein (7 kDa, Protein from Halorhodospira halochloris)
Trans-geranyl bacteriopheophytin b (885 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Reaction center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
Unknown ligand (909 Da, Ligand)
Trans-geranyl 8-vinyl-bacteriochlorophyll b (907 Da, Ligand)
Beta subunit of light-harvesting 1 (9 kDa, Protein from Halorhodospira halochloris)
2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
Gamma subunit of light-harvesting 1 (3 kDa, Protein from Halorhodospira halochloris)
Reaction center protein m chain (36 kDa, Protein from Halorhodospira halochloris)
Reaction center protein l chain (31 kDa, Protein from Halorhodospira halochloris)
Menaquinone 8 (717 Da, Ligand)
Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Halorhodospira halochloris)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
Ubiquinone-8 (727 Da, Ligand)
Heme c (618 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Antenna complex alpha/beta subunit domain-containing protein (12 kDa, Protein from Halorhodospira halochloris)
Lycopene (536 Da, Ligand)
Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
Reactin center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)

[Show more]

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EMDB [4]

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