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Structure of C2S2-type PSII-FCPII supercomplex from diatom
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 ]
- 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)
Structure of C2S1M1-type PSII-FCPII supercomplex from diatom
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 ]
- 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)
Structure of C2S2M2-type PSII-FCPII supercomplex from diatom
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 ]
- 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)