Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 9k3q
Q-score: 0.534
To Be Published
- Reaction center_light harvesting complex 1 from rhodospirillum rubrum (Complex from Rhodospirillum rubrum)
- Ubiquinone-10 (863 Da, Ligand)
- Trans-geranyl bacteriochlorophyll a (901 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (5 kDa, Protein from Rhodospirillum rubrum)
- Fe (iii) ion (55 Da, Ligand)
- Reaction center protein l chain (30 kDa, Protein from Rhodospirillum rubrum)
- Bacteriopheophytin a (889 Da, Ligand)
- Photoreaction center protein h (27 kDa, Protein from Rhodospirillum rubrum)
- Reaction center protein m chain (29 kDa, Protein from Rhodospirillum rubrum)
- Spirilloxanthin (596 Da, Ligand)
- Light-harvesting protein b-870 beta chain (5 kDa, Protein from Rhodospirillum rubrum)
Cryo-EM structure of Light-harvesting complex from Spinacia oleracea
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8y15
Q-score: 0.709
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ DOI: doi:10.1093/pnasnexus/pgae405 Pubmed: 39346626 ]
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- Water (18 Da, Ligand)
- Light-harvesting complex ii from spinacia oleracea (700 kDa, Complex from Spinacia oleracea)
- Lutein (568 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (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)
- (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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
Cryo-EM structure of in vitro reconstituted Light-harvesting complex II trimer
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yee
Q-score: 0.678
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ DOI: doi:10.1093/pnasnexus/pgae405 Pubmed: 39346626 ]
- Water (18 Da, Ligand)
- Lutein (568 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (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 (24 kDa, Protein from Spinacia oleracea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- In vitro reconstituted light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
- Chlorophyll a (893 Da, Ligand)
Cryo-EM structure of light-harvesting complex II with C1 symmetry
Seki S, Miyata T, Norioka N, Tanaka H, Kurisu G, Namba K, Fujii R
Pnas Nexus (2024) 3 pp. pgae405-pgae405 [ DOI: doi:10.1093/pnasnexus/pgae405 Pubmed: 39346626 ]
- Light-harvesting complex ii (120 kDa, Complex from Spinacia oleracea)
Cryo-EM structure of in vitro reconstituted LHCII with C1 symmetry
Bry-LHCII homotrimer of Bryopsis corticulans
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 8hlv
Q-score: 0.608
Li Z, Zhou C, Zhao S, Zhang J, Liu X, Sang M, Qin X, Yang Y, Han G, Kuang T, Shen JR, Wang W
Structure (2023) 31 pp. 1247- [ Pubmed: 37633266 DOI: doi:10.1016/j.str.2023.08.001 ]
- Chlorophyll a (893 Da, Ligand)
- Bryopsis corticulans chlorophyll a/b-type light-harvesting complex ii homotrimer (Complex from Bryopsis corticulans)
- Siphonaxanthin chlorophyll a/b binding light-harvesting complex ii, bry-lhcb1 (26 kDa, Protein from Bryopsis corticulans)
- Siphonaxanthin (600 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Siphonein (781 Da, Ligand)
Bry-LHCII heterotrimer of Bryopsis corticulans
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8hpd
Q-score: 0.571
Li Z, Zhou C, Zhao S, Zhang J, Liu X, Sang M, Qin X, Yang Y, Han G, Kuang T, Shen JR, Wang W
Structure (2023) 31 pp. 1247-1258.e3 [ Pubmed: 37633266 DOI: doi:10.1016/j.str.2023.08.001 ]
- Chlorophyll a (893 Da, Ligand)
- Bryopsis corticulans chlorophyll a/b-type light-harvesting complex ii heterotrimer (Complex from Bryopsis corticulans)
- Siphonaxanthin chlorophyll a/b binding light-harvesting complex ii, bry-lhcb1 (26 kDa, Protein from Bryopsis corticulans)
- Chlorophyll b (907 Da, Ligand)
- Siphonaxanthin (600 Da, Ligand)
- Siphonaxanthin chlorophyll a/b binding light-harvesting complex ii, bry-lhcb3 (27 kDa, Protein from Bryopsis corticulans)
- (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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Siphonaxanthin chlorophyll a/b binding light-harvesting complex ii, bry-lhcb2 (27 kDa, Protein from Bryopsis corticulans)
- Siphonein (781 Da, Ligand)
Resolution: 2.785 Å
EM Method: Single-particle
Fitted PDBs: 8c29
Q-score: 0.594
Opatikova M, Semchonok DA, Kopecny D, Ilik P, Pospisil P, Ilikova I, Roudnicky P, Zeljkovic SC, Tarkowski P, Kyrilis FL, Hamdi F, Kastritis PL, Kouril R
Nat Plants (2023) 9 pp. 1359-1369 [ DOI: doi:10.1038/s41477-023-01483-0 Pubmed: 37550369 ]
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Picea abies)
- Beta-carotene (536 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Picea abies)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (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)
- (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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (32 kDa, Protein from Picea abies)
- The c2s2-type psii-lhcii supercomplex (Complex from Picea abies)
- Photosystem ii core complex (c2) (Complex from Picea abies)
- Photosystem ii psbx (12 kDa, Protein from Picea abies)
- Magnesium ion (24 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Picea abies)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Picea abies)
- Palmitoleic acid (254 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Picea abies)
- Oxygen-evolving enhancer protein 1, chloroplastic (36 kDa, Protein from Picea abies)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Picea abies)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Picea abies)
- Photosystem ii 5 kda protein, chloroplastic (14 kDa, Protein from Picea abies)
- Alpha-linolenic acid (278 Da, Ligand)
- Photosystem ii cp43 reaction center protein (51 kDa, Protein from Picea abies)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (6 kDa, Protein from Picea abies)
- Photosystem ii reaction center protein i (4 kDa, Protein from Picea abies)
- Photosystem ii light-harvesting complex (Complex from Picea abies)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Picea abies)
- Photosystem ii reaction center protein m (3 kDa, Protein from Picea abies)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Picea abies)
- Chlorophyll a (893 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Water (18 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (32 kDa, Protein from Picea abies)
- Photosystem ii reaction center protein t (3 kDa, Protein from Picea abies)
- 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)
- (2r)-2,5,7,8-tetramethyl-2-[(4r,8r)-4,8,12-trimethyltridecyl]chroman-6-ol (430 Da, Ligand)
- Photosystem ii protein d1 (38 kDa, Protein from Picea abies)
- Psii 6.1 kda protein (15 kDa, Protein from Picea abies)
Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7yca
Q-score: 0.514
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ DOI: doi:10.7554/eLife.84488 Pubmed: 36951548 ]
- Chlorophyll c2 (608 Da, Ligand)
- Photosystem i-light-harvesting complex i-prasinophyte-specific lhc protein (psi-lhci-lhcp) supercomplex (Complex from Ostreococcus tauri)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (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)
- (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)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Ostreococcus tauri)
- Photosystem i psan, reaction centre subunit n (14 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Ostreococcus tauri)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction centre subunit iv (11 kDa, Protein from Ostreococcus tauri)
- Photosystem i psag/psak protein (13 kDa, Protein from Ostreococcus tauri)
- Lhca1 (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Ostreococcus tauri)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Ostreococcus tauri)
- Chlorophyll b (907 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iii (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Ostreococcus tauri)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Ostreococcus tauri)
- Psao (15 kDa, Protein from Ostreococcus tauri)
- Psi subunit v (21 kDa, Protein from Ostreococcus tauri)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Ostreococcus tauri)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Lhca6 (26 kDa, Protein from Ostreococcus tauri)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Ostreococcus tauri)
- Psag (14 kDa, Protein from Ostreococcus tauri)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i psah, reaction centre subunit vi (17 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Ostreococcus tauri)
- Photosystem i reaction center subunit ii, chloroplastic (20 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a isomer (893 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8hg5
Q-score: 0.486
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J
eLife (2023) 12 [ DOI: doi:10.7554/eLife.84488 Pubmed: 36951548 ]
- Chlorophyll c2 (608 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Ostreococcus tauri)
- (1~{s})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol (570 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-1-[(1~{s},4~{s})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{r},4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one (600 Da, Ligand)
- Cryo-em structure of the prasinophyte-specific light-harvesting complex (lhcp)from ostreococcus tauri (Complex from Ostreococcus tauri)
- (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 (24 kDa, Protein from Ostreococcus tauri)
- Chlorophyll a (893 Da, Ligand)