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Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8to2
Q-score: 0.592
Sauer PV, Cupellini L, Sutter M, Bondanza M, Dominguez Martin MA, Kirst H, Bina D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polivka T, Mennucci B, Kerfeld CA
Sci Adv (2024) 10 pp. eadk7535-eadk7535 [ DOI: doi:10.1126/sciadv.adk7535 Pubmed: 38578996 ]
- Complex of phycobilisome from synechocystis pcc 6803 bound to ocp (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin subunit beta-18 (18 kDa, Protein from Synechocystis sp. PCC 6803)
- Translation initiation factor if-2 (12 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin subunit alpha-b (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803)
Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8tpj
Q-score: 0.675
Sauer PV, Cupellini L, Sutter M, Bondanza M, Dominguez Martin MA, Kirst H, Bina D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polivka T, Mennucci B, Kerfeld CA
Sci Adv (2024) 10 pp. eadk7535-eadk7535 [ DOI: doi:10.1126/sciadv.adk7535 Pubmed: 38578996 ]
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome bound to ocp (Complex from Synechocystis sp. PCC 6803)
- Water (18 Da, Ligand)
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803)
Rod from high-resolution phycobilisome quenched by OCP (local refinement)
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 8tro
Q-score: 0.791
Sauer PV, Cupellini L, Sutter M, Bondanza M, Dominguez Martin MA, Kirst H, Bina D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polivka T, Mennucci B, Kerfeld CA
Sci Adv (2024) 10 pp. eadk7535-eadk7535 [ DOI: doi:10.1126/sciadv.adk7535 Pubmed: 38578996 ]
- Phycobilisome rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycocyanobilin (588 Da, Ligand)
- Phycobilisome 8.9 kda linker polypeptide, phycocyanin-associated, rod (9 kDa, Protein from Synechocystis sp. PCC 6803)
- C-phycocyanin alpha subunit (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 2 (30 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome bound to ocp (Complex from Synechocystis sp. PCC 6803)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (32 kDa, Protein from Synechocystis sp. PCC 6803)
- Water (18 Da, Ligand)
- C-phycocyanin beta subunit (18 kDa, Protein from Synechocystis sp. PCC 6803)
Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8hfq
Q-score: 0.621
Zheng L, Zhang Z, Wang H, Zheng Z, Wang J, Liu H, Chen H, Dong C, Wang G, Weng Y, Gao N, Zhao J
Nat Commun (2023) 14 pp. 3961-3961 [ Pubmed: 37407580 DOI: doi:10.1038/s41467-023-39689-7 ]
- Ferredoxin--nadp reductase (46 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (32 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycocyanobilin (588 Da, Ligand)
- Cryo-em structure of cpcl-pbs from cyanobacterium synechocystis sp. pcc 6803 (Complex from Synechocystis sp. PCC 6803)
- Photosystem i-associated linker protein cpcl (28 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 2 (30 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- C-phycocyanin alpha subunit (17 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- C-phycocyanin beta subunit (18 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8am5
Q-score: 0.52
Zhao Z, Vercellino I, Knoppova J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J
Nat Commun (2023) 14 pp. 4681-4681 [ Pubmed: 37542031 DOI: doi:10.1038/s41467-023-40388-6 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii assembly lipoprotein ycf48 (37 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a isomer (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Rcii/psi complex (Complex from Synechocystis sp. PCC 6803)
- Phylloquinone (450 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii d2 protein (37 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a (893 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- (3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8asl
Q-score: 0.518
Zhao Z, Vercellino I, Knoppova J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J
Nat Commun (2023) 14 pp. 4681-4681 [ Pubmed: 37542031 DOI: doi:10.1038/s41467-023-40388-6 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii assembly lipoprotein ycf48 (37 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a isomer (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Rcii/psi complex class 2 (Complex from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Phylloquinone (450 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii d2 protein (37 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
- Chlorophyll a (893 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- (3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Oligomeric structure of SynDLP
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7zw6
Q-score: 0.221
Cryo-EM structure of Synechocystis sp. PCC 6803 RPitc
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8gzg
Q-score: 0.488
PNAS (2023) [ ]
- The complex of synechocystis sp. pcc 6803 rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Template strand dna (20 kDa, DNA from synthetic construct)
- Rna polymerase sigma factor siga (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Synechocystis sp. PCC 6803)
- Rna (5'-r(*up*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8gzh
Q-score: 0.534
PNAS (2023) [ ]
- Template strand dna (20 kDa, DNA from synthetic construct)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Rna polymerase sigma factor siga (50 kDa, Protein from Synechocystis sp. PCC 6803)
- Nontemplate strand dna (20 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit beta' (145 kDa, Protein from Synechocystis sp. PCC 6803)
- The complex of synechocystis sp. pcc 6803 ctp-bound rpitc (500 kDa, Complex from Synechocystis sp. PCC 6803)
- Magnesium ion (24 Da, Ligand)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechocystis sp. PCC 6803)
Resolution: 1.93 Å
EM Method: Single-particle
Fitted PDBs: 7n8o
Q-score: 0.708
Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW
PNAS (2022) 119 [ DOI: doi:10.1073/pnas.2116765118 Pubmed: 34937700 ]
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii 12 kda extrinsic protein (14 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii d2 protein (39 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Water (18 Da, Ligand)
- Photosystem ii reaction center x protein (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Calcium ion (40 Da, Ligand)
- Photosystem ii protein d1 2 (39 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii (Complex from Synechocystis sp. PCC 6803)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- 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 cp43 reaction center protein (50 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein m (3 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Chloride ion (35 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein j (3 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii protein y (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein k (5 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Cytochrome c-550 (17 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein h (7 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Pheophytin a (871 Da, Ligand)
- Sll1638 protein (16 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- 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 Synechocystis sp. (strain PCC 6803 / Kazusa))
- Photosystem ii reaction center protein z (6 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Fe (ii) ion (55 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Dodecyl-beta-d-maltoside (510 Da, Ligand)