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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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author:"Kato K" AND author_name:"Hamaguchi T" AND natural_source_ncbi_code:"32053"

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EMD-31062

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Structure of monomeric photosystem II

Release date: July 7, 2021
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 7eda
Q-score: 0.622

Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR

Biochim Biophys Acta Bioenerg (2021) 1862 pp. 148471-148471 [ Pubmed: 34216574 DOI: doi:10.1016/j.bbabio.2021.148471 ]

Sample:

Unknown ligand (949 Da, Ligand)
Photosystem ii (Complex from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein h (6 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein j (4 kDa, Protein from Thermosynechococcus vulcanus)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Beta-carotene (536 Da, Ligand)
Cytochrome c-550 (18 kDa, Protein from Thermosynechococcus vulcanus)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Heme c (618 Da, Ligand)
Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
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)
(3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
Cytochrome b559 subunit beta (5 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii 12 kda extrinsic protein (11 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
Pheophytin a (871 Da, Ligand)
Ca-mn4-o5 cluster (339 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
Chlorophyll a (893 Da, Ligand)
Photosystem ii cp47 reaction center protein (55 kDa, Protein from Thermosynechococcus vulcanus)
Fe (ii) ion (55 Da, Ligand)
Water (18 Da, Ligand)
Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)

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EMD-30547

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Cryo-EM Structure of PSII at 1.95 angstrom resolution

Release date: March 31, 2021
Resolution: 1.95 Å
EM Method: Single-particle
Fitted PDBs: 7d1t
Q-score: 0.776

Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR

Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]

Sample:

Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Fe (ii) ion (55 Da, Ligand)
Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
Chlorophyll a (893 Da, Ligand)
Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
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)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
Beta-carotene (536 Da, Ligand)
Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
Ca-mn4-o5 cluster (339 Da, Ligand)
Heme c (618 Da, Ligand)
Water (18 Da, Ligand)
Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Unknown ligand (Ligand)
Chloride ion (35 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
Bicarbonate ion (61 Da, Ligand)
(3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)

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EMD-30548

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Cryo-EM Structure of PSII at 2.08 angstrom resolution

Release date: March 31, 2021
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 7d1u
Q-score: 0.757

Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR

Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]

Sample:

1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Beta-carotene (536 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
Heme c (618 Da, Ligand)
Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
Protoporphyrin ix containing fe (616 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
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)
Unknown ligand (Ligand)
(3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
Chloride ion (35 Da, Ligand)
Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
Pheophytin a (871 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
Ca-mn4-o5 cluster (339 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
Chlorophyll a (893 Da, Ligand)
Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
Fe (ii) ion (55 Da, Ligand)
Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
Water (18 Da, Ligand)
Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Dodecyl-beta-d-maltoside (510 Da, Ligand)

[Show more]

EMD-30549

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Cryo-EM Structure of PSII at 2.22 angstrom resolution

Release date: March 31, 2021
Resolution: 2.22 Å
EM Method: Single-particle

Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR

Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]

Sample:

Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)

EMD-30550

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Cryo-EM Structure of PSII at 2.20 angstrom resolution

Release date: March 31, 2021
Resolution: 2.2 Å
EM Method: Single-particle

Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR

Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]

Sample:

Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)

Sort by: Download

Showing 1 - 5 of 5. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [5]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

Field: