Cryo-EM Structure of native Photosystem II assembly intermediate fromChlamydomonas reinhardtii
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8r2i
Q-score: 0.533
Fadeeva M, Klaiman D, Kandiah E, Nelson N
Front Plant Sci (2023) 14 pp. 1334608-1334608 [ Pubmed: 38322422 DOI: doi:10.3389/fpls.2023.1334608 ]
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii assembly intermediate from chlamydomonas reinhardtii (Complex from Chlamydomonas reinhardtii)
- Octyl beta-d-glucopyranoside (292 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii protein d1 (36 kDa, Protein from Chlamydomonas reinhardtii)
- 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 cp43 reaction center protein (46 kDa, Protein from Chlamydomonas reinhardtii)
- Beta-carotene (536 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Chain u, predicted protein (11 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chlamydomonas reinhardtii)
- Water (18 Da, Ligand)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Chlamydomonas reinhardtii)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein i (3 kDa, Protein from Chlamydomonas reinhardtii)
PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 7xqp
Q-score: 0.536
Zhang S, Tang K, Yan Q, Li X, Shen L, Wang W, He YK, Kuang T, Han G, Shen JR, Zhang X
Nat Plants (2023) 9 pp. 832-846 [ Pubmed: 37095225 DOI: doi:10.1038/s41477-023-01401-4 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Physcomitrium patens)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Physcomitrium patens)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Physcomitrium patens)
- Psao (9 kDa, Protein from Physcomitrium patens)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Physcomitrium patens)
- Psi-g (10 kDa, Protein from Physcomitrium patens)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Physcomitrium patens)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Physcomitrium patens)
- Psae (6 kDa, Protein from Physcomitrium patens)
- Chlorophyll a-b binding protein, chloroplastic (20 kDa, Protein from Physcomitrium patens)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Physcomitrium patens)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Physcomitrium patens)
- Psah photosystem i reaction center subunit (10 kDa, Protein from Physcomitrium patens)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Physcomitrium patens)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Physcomitrium patens)
- Psi-lhci-lhcii-lhcb9 supercomplex of physcomitrella patens (Complex from Physcomitrium patens)
- Psi subunit v (17 kDa, Protein from Physcomitrium patens)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Psi-f (17 kDa, Protein from Physcomitrium patens)
- Predicted protein psad (15 kDa, Protein from Physcomitrium patens)
- Psak (8 kDa, Protein from Physcomitrium patens)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Physcomitrium patens)
PSI-LHCI Supercomplex from Physcometrella patens
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 6l35
Q-score: 0.545
Yan Q, Zhao L, Wang W, Pi X, Han G, Wang J, Cheng L, He YK, Kuang T, Qin X, Sui SF, Shen JR
Cell Discov (2021) 7 pp. 10-10 [ DOI: doi:10.1038/s41421-021-00242-9 Pubmed: 33589616 ]
- Phylloquinone (450 Da, Ligand)
- Psi subunit v (16 kDa, Protein from Moss)
- Predicted protein psad (15 kDa, Protein from Moss)
- Psah photosystem i reaction center subunit (9 kDa, Protein from Moss)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Psak (7 kDa, Protein from Moss)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Moss)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Moss)
- Chlorophyll a-b binding protein, chloroplastic (20 kDa, Protein from Moss)
- Beta-carotene (536 Da, Ligand)
- Psi-lhci (Complex from Physcomitrella patens)
- Psi-f (17 kDa, Protein from Moss)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Moss)
- Iron/sulfur cluster (351 Da, Ligand)
- Predicted protein psag (10 kDa, Protein from Moss)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Moss)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Moss)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psae (6 kDa, Protein from Moss)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Moss)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Moss)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Moss)
- Photosystem i iron-sulfur center (8 kDa, Protein from Moss)
Composite cryo-EM density map of the radial spoke 1 isolated from Chlamydomonas reinhardtii
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7jtk
Q-score: 0.501
Gui M, Ma M, Sze-Tu E, Wang X, Koh F, Zhong ED, Berger B, Davis JH, Dutcher SK, Zhang R, Brown A
Nat Struct Mol Biol (2021) 28 pp. 29-37 [ DOI: doi:10.1038/s41594-020-00530-0 Pubmed: 33318703 ]
- Predicted protein (8 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 3 (56 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b5 heme-binding domain-containing protein (26 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 11 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 12 (19 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 9 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 23 (61 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 1 (87 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 2 (77 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (2 kDa, Protein from Chlamydomonas reinhardtii)
- Phosphate ion (94 Da, Ligand)
- Flagellar radial spoke protein 16 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Uncharacterized protein (75 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 14 (40 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 10 (23 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 7 (54 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 5 (55 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 4 (49 kDa, Protein from Chlamydomonas reinhardtii)
- Radial spoke 1 (Complex from Chlamydomonas reinhardtii)
- Dynein 8 kda light chain, flagellar outer arm (10 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar radial spoke protein 6 (48 kDa, Protein from Chlamydomonas reinhardtii)
NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6qve
Q-score: 0.435
Atherton J, Luo Y, Xiang S, Yang C, Rai A, Jiang K, Stangier M, Vemu A, Cook AD, Wang S, Roll-Mecak A, Steinmetz MO, Akhmanova A, Baldus M, Moores CA
Nat Commun (2019) 10 pp. 5236-5236 [ DOI: doi:10.1038/s41467-019-13247-6 Pubmed: 31748546 ]
- Tubulin alpha-1b chain (50 kDa, Protein from Homo sapiens)
- Predicted protein (20 kDa, Protein from Naegleria gruberi)
- Tubulin (Complex from Homo sapiens)
- Ngckk (naegleria gruberi ckk) decorated 14pf taxol-gdp microtubule (Complex)
- Taxol (853 Da, Ligand)
- Naegleria gruberi ckk (Complex from Naegleria gruberi)
- Beta1-tubulin (49 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6kac
Q-score: 0.569
Sheng X, Watanabe A, Li A, Kim E, Song C, Murata K, Song D, Minagawa J, Liu Z
Nat Plants (2019) 5 pp. 1320-1330 [ DOI: doi:10.1038/s41477-019-0543-4 Pubmed: 31768031 ]
- Oxygen-evolving enhancer protein 3, chloroplastic (21 kDa, Protein from Chlamydomonas reinhardtii)
- Predicted protein (19 kDa, Protein from Chlamydomonas reinhardtii)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Oxygen-evolving enhancer protein 2, chloroplastic (25 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll b (907 Da, Ligand)
- The c2s2-type psii-lhcii supercomplex (Complex from Chlamydomonas reinhardtii)
- Unindentified stromal protein (usp) (2 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Chlamydomonas reinhardtii)
- 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)
- Beta-carotene (536 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Oxygen-evolving enhancer protein 1, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
- 10 kda photosystem ii polypeptide psbr (potential) (1 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Water (18 Da, Ligand)
- Photosystem ii reaction center w protein, chloroplastic (12 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- 4.1 kda photosystem ii subunit (9 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein cp29 (29 kDa, Protein from Chlamydomonas reinhardtii)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein j (4 kDa, Protein from Chlamydomonas reinhardtii)
Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in nanodisc
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6qm4
Q-score: 0.415
Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C
eLife (2019) 8 [ DOI: doi:10.7554/eLife.44364 Pubmed: 30785398 ]
- Predicted protein (83 kDa, Protein from Nectria haematococca)
- Nhtmem16 (166 kDa, Complex from Nectria haematococca mpVI 77-13-4)
Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in DDM
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6qm5
Q-score: 0.494
Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C
eLife (2019) 8 [ DOI: doi:10.7554/eLife.44364 Pubmed: 30785398 ]
- Predicted protein (83 kDa, Protein from Nectria haematococca)
- Calcium ion (40 Da, Ligand)
- Nhtmem16 (166 kDa, Complex from Nectria haematococca mpVI 77-13-4)
Cryo-EM structure of calcium-free nhTMEM16 lipid scramblase in DDM
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6qm6
Q-score: 0.467
Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C
eLife (2019) 8 [ DOI: doi:10.7554/eLife.44364 Pubmed: 30785398 ]
- Predicted protein (83 kDa, Protein from Nectria haematococca)
- Nhtmem16 (166 kDa, Complex from Nectria haematococca mpVI 77-13-4)
Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (open state)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6qm9
Q-score: 0.46
Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C
eLife (2019) 8 [ DOI: doi:10.7554/eLife.44364 Pubmed: 30785398 ]
- Predicted protein (83 kDa, Protein from Nectria haematococca)
- Calcium ion (40 Da, Ligand)
- Nhtmem16 (166 kDa, Complex from Nectria haematococca mpVI 77-13-4)