Cryo-EM structure of cryptophyte photosystem II
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8xr6
Q-score: 0.574
Zhang YZ, Li K, Qin BY, Guo JP, Zhang QB, Zhao DL, Chen XL, Gao J, Liu LN, Zhao LS
Nat Commun (2024) 15 pp. 4999-4999 [ DOI: doi:10.1038/s41467-024-49453-0 Pubmed: 38866834 ]
- Fe (ii) ion (55 Da, Ligand)
- Psbc_cp43 (52 kDa, Protein from Chroomonas placoidea)
- Photosystem ii protein d1 (39 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chroomonas placoidea)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chroomonas placoidea)
- Acpii-2 (22 kDa, Protein from Chroomonas placoidea)
- Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chroomonas placoidea)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Acpii-6 (25 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein psb30 (3 kDa, Protein from Chroomonas placoidea)
- Psbo (32 kDa, Protein from Chroomonas placoidea)
- Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Water (18 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chroomonas placoidea)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psbm (3 kDa, Protein from Chroomonas placoidea)
- Acpii-1 (23 kDa, Protein from Chroomonas placoidea)
- Psb-gama_linker (31 kDa, Protein from Chroomonas placoidea)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chloride ion (35 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)
- Photosystem ii of cryptophyte (1 MDa, Complex from Chroomonas placoidea)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chroomonas placoidea)
- Psbw (13 kDa, Protein from Chroomonas placoidea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psbu (13 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Chroomonas placoidea)
- Photosystem ii cytochrome c550 (17 kDa, Protein from Chroomonas placoidea)
- Psbq (15 kDa, Protein from Chroomonas placoidea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein x (4 kDa, Protein from Chroomonas placoidea)
Structure of PSII-ACPII supercomplex from cryptophyte algae
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 8wb4
Q-score: 0.539
Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G
Nat Commun (2024) 15 pp. 4535-4535 [ Pubmed: 38806516 DOI: doi:10.1038/s41467-024-48878-x ]
- Photosystem ii protein d1 (39 kDa, Protein from Chroomonas placoidea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chroomonas placoidea)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein u (15 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Photosystem ii reaction center protein o (34 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein r (2 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein q (1 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein w (11 kDa, Protein from Chroomonas placoidea)
- Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chroomonas placoidea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chroomonas placoidea)
- Structure of psii-acpii supercomplex from cryptophyte algae (Complex from Chroomonas placoidea)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chroomonas placoidea)
- Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center m (11 kDa, Protein from Chroomonas placoidea)
- Photosystem ii d2 protein (39 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center x protein (4 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
- Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chroomonas placoidea)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chroomonas placoidea)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chroomonas placoidea)
- 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)
- Acpii-2 (23 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
- Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
- Chloride ion (35 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii cytochrome c550 (17 kDa, Protein from Chroomonas placoidea)
Structure of ACPII-CCPII from cryptophyte algae
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8xkl
Q-score: 0.49
Mao Z, Li X, Li Z, Shen L, Li X, Yang Y, Wang W, Kuang T, Shen JR, Han G
Nat Commun (2024) 15 pp. 4535-4535 [ Pubmed: 38806516 DOI: doi:10.1038/s41467-024-48878-x ]
- Acpii-3 (24 kDa, Protein from Chroomonas placoidea)
- Acpii-2 (23 kDa, Protein from Chroomonas placoidea)
- Acpii-5 (23 kDa, Protein from Chroomonas placoidea)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Acpii-1 (25 kDa, Protein from Chroomonas placoidea)
- Acpii-6 (23 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Photosystem ii reaction center protein g (5 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Acpii-4 (23 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- (1~{r})-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-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Ccpii-s (30 kDa, Protein from Chroomonas placoidea)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Structure of acpii-ccpii from cryptophyte algae (Complex from Chroomonas placoidea)
Cryo-EM structure of cryptophyte photosystem I
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 7y7b
Q-score: 0.607
Zhao LS, Wang P, Li K, Zhang QB, He FY, Li CY, Su HN, Chen XL, Liu LN, Zhang YZ
Plant Cell (2023) 35 pp. 2449-2463 [ DOI: doi:10.1093/plcell/koad087 Pubmed: 36943796 ]
- Photosystem i of cryptophyte (890 kDa, Complex from Chroomonas placoidea)
- (1~{r})-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-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psao (10 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chroomonas placoidea)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chroomonas placoidea)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Acpi-11 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- Acpi-13/10 (22 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-9 (27 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Cryo-EM structure of cryptophyte photosystem I
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 7y8a
Q-score: 0.581
Zhao LS, Wang P, Li K, Zhang QB, He FY, Li CY, Su HN, Chen XL, Liu LN, Zhang YZ
Plant Cell (2023) 35 pp. 2449-2463 [ DOI: doi:10.1093/plcell/koad087 Pubmed: 36943796 ]
- Photosystem i of cryptophyte (Complex from Chroomonas placoidea)
- (1~{r})-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-octaen-1-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chroomonas placoidea)
- Acpi-6 (22 kDa, Protein from Chroomonas placoidea)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chroomonas placoidea)
- Acpi-2 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chroomonas placoidea)
- Acpi-8 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chroomonas placoidea)
- Acpi-3 (24 kDa, Protein from Chroomonas placoidea)
- Psar (13 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chroomonas placoidea)
- (1~{r})-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-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol (550 Da, Ligand)
- Unk1 (13 kDa, Protein from Chroomonas placoidea)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol (564 Da, Ligand)
- Acpi-13 (22 kDa, Protein from Chroomonas placoidea)
- Acpi-s (25 kDa, Protein from Chroomonas placoidea)
- Acpi-12 (23 kDa, Protein from Chroomonas placoidea)
- Acpi-5 (24 kDa, Protein from Chroomonas placoidea)
- Chlorophyll a (893 Da, Ligand)
- Acpi-7 (24 kDa, Protein from Chroomonas placoidea)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chroomonas placoidea)
- Psao (16 kDa, Protein from Chroomonas placoidea)
- Acpi-14 (23 kDa, Protein from Chroomonas placoidea)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Chroomonas placoidea)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Chroomonas placoidea)
- Acpi-1 (23 kDa, Protein from Chroomonas placoidea)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chroomonas placoidea)
- Acpi-4 (23 kDa, Protein from Chroomonas placoidea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chroomonas placoidea)
- Chlorophyll c2 (608 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)