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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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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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sample_formula:"DGD" AND author_name:"Akimoto S"

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EMD-31905

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Structure of C2S2M2-type PSII-FCPII supercomplex from diatom

Release date: March 2, 2022
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7vd5
Q-score: 0.543

Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR

Nat Commun (2022) 13 pp. 1764- [ DOI: doi:10.1038/s41467-022-29294-5 ]

Sample:

Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
Ca-mn4-o5 cluster (339 Da, Ligand)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
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)
Water (18 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
(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)
Unknown ligand (Ligand)
Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a (893 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
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)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Chlorophyll c1 (610 Da, Ligand)
C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)

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EMD-9775

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Structure of C2S2-type PSII-FCPII supercomplex from diatom

Release date: Aug. 7, 2019
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6j3y
Q-score: 0.503

Nagao R, Kato K, Suzuki T, Ifuku K, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F

Nat Plants (2019) 5 pp. 890-901 [ Pubmed: 31358960 DOI: doi:10.1038/s41477-019-0477-x ]

Sample:

Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
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)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Pheophytin a (871 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 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)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein m (14 kDa, Protein from Chaetoceros gracilis)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a (893 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
C2s2-type psii-fcpii supercomplex (850 kDa, Complex from Chaetoceros gracilis)

[Show more]

EMD-9776

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Structure of C2S1M1-type PSII-FCPII supercomplex from diatom

Release date: Aug. 7, 2019
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6j3z
Q-score: 0.444

Nagao R, Kato K, Suzuki T, Ifuku K, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F

Nat Plants (2019) 5 pp. 890-901 [ Pubmed: 31358960 DOI: doi:10.1038/s41477-019-0477-x ]

Sample:

Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
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)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein monomer 2 (12 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 1 (18 kDa, Protein from Chaetoceros gracilis)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Pheophytin a (871 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 3 (13 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 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)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein m (14 kDa, Protein from Chaetoceros gracilis)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a (893 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Bicarbonate ion (61 Da, Ligand)
C2s1m1-type psii-fcpii supercomplex (910 kDa, Complex from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)

[Show more]

EMD-9777

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Structure of C2S2M2-type PSII-FCPII supercomplex from diatom

Release date: Aug. 7, 2019
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6j40
Q-score: 0.349

Nagao R, Kato K, Suzuki T, Ifuku K, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F

Nat Plants (2019) 5 pp. 890-901 [ Pubmed: 31358960 DOI: doi:10.1038/s41477-019-0477-x ]

Sample:

Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
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)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein monomer 2 (12 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 1 (18 kDa, Protein from Chaetoceros gracilis)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Pheophytin a (871 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 3 (13 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 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)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein m (14 kDa, Protein from Chaetoceros gracilis)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a (893 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)

[Show more]

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EMDB [4]

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