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Tissue biology and disease modelling

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sample_formula:"DGD" AND author_name:"Akimoto S" AND assembly_molecular_weight:{1000000 TO 2000000]

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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:

Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Protoporphyrin ix containing fe (616 Da, Ligand)
Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
Water (18 Da, Ligand)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein w (5 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)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
Unknown ligand (Ligand)
Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
(3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Chlorophyll c1 (610 Da, Ligand)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
Bicarbonate ion (61 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Pheophytin a (871 Da, Ligand)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Fe (ii) ion (55 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex 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)

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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 i (4 kDa, Protein from Chaetoceros gracilis)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 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)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Cytochrome c-550 (14 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)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Pheophytin a (871 Da, Ligand)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
C2s2-type psii-fcpii supercomplex (850 kDa, Complex from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
Photosystem ii reaction center protein m (14 kDa, Protein 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 i (4 kDa, Protein from Chaetoceros gracilis)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 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)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 3 (13 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
Dodecyl-alpha-d-maltoside (510 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-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 2 (12 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 1 (18 kDa, Protein from Chaetoceros gracilis)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Pheophytin a (871 Da, Ligand)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
Photosystem ii reaction center protein m (14 kDa, Protein from Chaetoceros gracilis)
C2s1m1-type psii-fcpii supercomplex (910 kDa, Complex 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 i (4 kDa, Protein from Chaetoceros gracilis)
Protoporphyrin ix containing fe (616 Da, Ligand)
Photosystem ii chlorophyll protein cp47 (56 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein z (6 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)
Photosystem ii reaction center protein j (4 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
Photosystem ii chlorophyll protein cp43 (51 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 3 (13 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit alpha (9 kDa, Protein from Chaetoceros gracilis)
Cytochrome c-550 (14 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)
Dodecyl-alpha-d-maltoside (510 Da, Ligand)
1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
Photosystem ii reaction center protein w (7 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
Extrinsic protein in photosystem ii (17 kDa, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 2 (12 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d1 (38 kDa, Protein from Chaetoceros gracilis)
Cytochrome b559 subunit beta (4 kDa, Protein from Chaetoceros gracilis)
Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
Unknown protein 2 (869 Da, Protein from Chaetoceros gracilis)
Fucoxanthin chlorophyll a/c-binding protein monomer 1 (18 kDa, Protein from Chaetoceros gracilis)
Ca-mn4-o5 cluster (339 Da, Ligand)
Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
Photosystem ii reaction center protein d2 (39 kDa, Protein from Chaetoceros gracilis)
1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
Bicarbonate ion (61 Da, Ligand)
Chlorophyll a (893 Da, Ligand)
Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
Pheophytin a (871 Da, Ligand)
Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
Fe (ii) ion (55 Da, Ligand)
1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Fucoxanthin chlorophyll a/c-binding protein lhcf1, fcp1 (22 kDa, Protein from Chaetoceros gracilis)
Beta-carotene (536 Da, Ligand)
C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)
Photosystem ii reaction center protein m (14 kDa, Protein from Chaetoceros gracilis)

[Show more]

Sort by: Download

Showing 1 - 4 of 4. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [4]

Format:

Select the script type:

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

Preview first 10

Field: