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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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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 natural_source_ncbi_code:"1148"

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EMD-43843

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Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain

Release date: Dec. 25, 2024
Resolution: 2.03 Å
EM Method: Single-particle
Fitted PDBs: 9au4

Gisriel CJ, Kurashov V, Iwig DF, Russell BP, Vinyard DJ, Brudvig GW, Golbeck JH, Lakshmi KV

Sci Adv (2024) 10 pp. eadp4937-eadp4937 [ DOI: doi:10.1126/sciadv.adp4937 Pubmed: 39612342 ]

Sample:

Menb photosystem i (Complex from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta,beta-caroten-4-one (550 Da, Ligand)
Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
Beta-carotene (536 Da, Ligand)
Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
(1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Water (18 Da, Ligand)
Chloride ion (35 Da, Ligand)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
2,3-dimethyl-5-[(2e,7r,11r)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione (414 Da, Ligand)
Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem i reaction center subunit psak 2 (9 kDa, Protein from Synechocystis sp. PCC 6803)
Calcium ion (40 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
(3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)

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EMD-15522

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RCII/PSI complex, class 3

Release date: Aug. 16, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8am5
Q-score: 0.52

Zhao Z, Vercellino I, Knoppova J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J

Nat Commun (2023) 14 pp. 4681-4681 [ DOI: doi:10.1038/s41467-023-40388-6 Pubmed: 37542031 ]

Sample:

Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
Phylloquinone (450 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta,beta-caroten-4-one (550 Da, Ligand)
Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
Beta-carotene (536 Da, Ligand)
Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
Rcii/psi complex (Complex from Synechocystis sp. PCC 6803)
Fe (ii) ion (55 Da, Ligand)
(1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii d2 protein (37 kDa, Protein from Synechocystis sp. PCC 6803)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
Pheophytin a (871 Da, Ligand)
Chlorophyll a isomer (893 Da, Ligand)
Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
Protoporphyrin ix containing fe (616 Da, Ligand)
(3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
Photosystem ii assembly lipoprotein ycf48 (37 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)

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EMD-15618

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RCII/PSI complex, class 2

Release date: Aug. 16, 2023
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8asl
Q-score: 0.518

Zhao Z, Vercellino I, Knoppova J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J

Nat Commun (2023) 14 pp. 4681-4681 [ DOI: doi:10.1038/s41467-023-40388-6 Pubmed: 37542031 ]

Sample:

Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
Phylloquinone (450 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta,beta-caroten-4-one (550 Da, Ligand)
Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
Beta-carotene (536 Da, Ligand)
Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
Fe (ii) ion (55 Da, Ligand)
(1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii d2 protein (37 kDa, Protein from Synechocystis sp. PCC 6803)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
Pheophytin a (871 Da, Ligand)
Chlorophyll a isomer (893 Da, Ligand)
Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
Rcii/psi complex class 2 (Complex from Synechocystis sp. PCC 6803)
Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
Protoporphyrin ix containing fe (616 Da, Ligand)
(3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
Photosystem ii assembly lipoprotein ycf48 (37 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Iron/sulfur cluster (351 Da, Ligand)
Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)

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EMD-15621

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RCII/PSI complex, focused refinement of PSI

Release date: Aug. 16, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8asp
Q-score: 0.571

Zhao Z, Vercellino I, Knoppova J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J

Nat Commun (2023) 14 pp. 4681-4681 [ DOI: doi:10.1038/s41467-023-40388-6 Pubmed: 37542031 ]

Sample:

Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
Phylloquinone (450 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta,beta-caroten-4-one (550 Da, Ligand)
Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
Beta-carotene (536 Da, Ligand)
Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
Rcii/psi complex (Complex from Synechocystis sp. PCC 6803)
(1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
Chlorophyll a isomer (893 Da, Ligand)
Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
(3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
Iron/sulfur cluster (351 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Synechocystis sp. PCC 6803)

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EMD-14224

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2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

Release date: July 6, 2022
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7r0w
Q-score: 0.523

Proctor MS, Malone LA, Farmer DA, Swainsbury DJK, Hawkings FR, Pastorelli F, Emrich-Mills TZ, Siebert CA, Hunter CN, Johnson MP, Hitchcock A

Biochem J (2022) 479 pp. 1487-1503 [ Pubmed: 35726684 DOI: doi:10.1042/BCJ20220124 ]

Sample:

(4s,7r)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Cytochrome b6f complex in association with petp (Complex from Synechocystis sp. PCC 6803)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta,beta-caroten-4-one (550 Da, Ligand)
Uncharacterized protein cp097, conserved in cyanobacteria (7 kDa, Protein from Synechocystis)
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)
Heme c (618 Da, Ligand)
Cytochrome b6-f complex subunit 5 (4 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6-f complex subunit 4 (17 kDa, Protein from Synechocystis sp. PCC 6803)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
Water (18 Da, Ligand)
Cytochrome b6-f complex subunit 7 (3 kDa, Protein from Synechocystis sp. PCC 6803)
(1s,8e)-1-{[(2s)-1-hydroxy-3-{[(1s)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol (570 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Rieske domain, petc (20 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6 (25 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome f (35 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6 (3 kDa, Protein from Synechocystis sp. PCC 6803)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome b6-f complex subunit 8 (3 kDa, Protein from Synechocystis sp. PCC 6803)
Chlorophyll a (893 Da, Ligand)
Eicosane (282 Da, Ligand)

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EMD-15017

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3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Synechocystis sp. PCC 6803 with natively bound plastoquinone and lipid molecules.

Release date: July 6, 2022
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7zxy
Q-score: 0.54

Proctor MS, Malone LA, Farmer DA, Swainsbury DJK, Hawkings FR, Pastorelli F, Emrich-Mills TZ, Siebert CA, Hunter CN, Johnson MP, Hitchcock A

Biochem J (2022) 479 pp. 1487-1503 [ Pubmed: 35726684 DOI: doi:10.1042/BCJ20220124 ]

Sample:

Cytochrome b6 (25 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6 (3 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6-f complex iron-sulfur subunit 2 (19 kDa, Protein from Synechocystis sp. PCC 6803)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome b6-f complex subunit 7 (3 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome b6-f complex subunit 5 (4 kDa, Protein from Synechocystis sp. PCC 6803)
Beta,beta-caroten-4-one (550 Da, Ligand)
Cytochrome b6f with natively associated lipids and plastoquinone (Complex from Synechocystis sp. PCC 6803)
Cytochrome b6-f complex subunit 8 (3 kDa, Protein from Synechocystis sp. PCC 6803)
Cytochrome f (30 kDa, Protein from Synechocystis sp. PCC 6803)
Chlorophyll a (893 Da, Ligand)
Eicosane (282 Da, Ligand)
Cytochrome b6-f complex subunit 4 (17 kDa, Protein from Synechocystis sp. PCC 6803)
Heme c (618 Da, Ligand)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)

[Show more]

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