Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eoz
Q-score: 0.465
Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C
Nat Commun (2024) 15 pp. 9407-9407 [ DOI: doi:10.1038/s41467-024-53811-3 Pubmed: 39477986 ]
- Widom 601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Widom 601 dna (145-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome core particle (Complex from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (Complex from synthetic construct)
- Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle (Complex)
- N-glycosylase/dna lyase (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris
Qi CH, Wang GL, Wang FF, Wang J, Wang XP, Zou MJ, Ma F, Madigan MT, Kimura Y, Wang-Otomo ZY, Yu LJ
J Integr Plant Biol (2024) 66 pp. 2262-2272 [ DOI: doi:10.1111/jipb.13628 Pubmed: 38411333 ]
- Light-harvesting lhi (7 kDa, Protein from Halorhodospira halochloris)
- Cardiolipin (1 kDa, Ligand)
- Trans-geranyl bacteriochlorophyll b (907 Da, Ligand)
- Rc-lh core complex (Complex from Halorhodospira halochloris)
- Photosynthetic reaction center h subunit (31 kDa, Protein from Halorhodospira halochloris)
- Antenna complex alpha/beta subunit domain-containing protein (7 kDa, Protein from Halorhodospira halochloris)
- Trans-geranyl bacteriopheophytin b (885 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Reaction center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Unknown ligand (909 Da, Ligand)
- Trans-geranyl 8-vinyl-bacteriochlorophyll b (907 Da, Ligand)
- Beta subunit of light-harvesting 1 (9 kDa, Protein from Halorhodospira halochloris)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Gamma subunit of light-harvesting 1 (3 kDa, Protein from Halorhodospira halochloris)
- Reaction center protein m chain (36 kDa, Protein from Halorhodospira halochloris)
- Reaction center protein l chain (31 kDa, Protein from Halorhodospira halochloris)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Halorhodospira halochloris)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Ubiquinone-8 (727 Da, Ligand)
- Heme c (618 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Antenna complex alpha/beta subunit domain-containing protein (12 kDa, Protein from Halorhodospira halochloris)
- Lycopene (536 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Reactin center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
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 [ Pubmed: 38578996 DOI: doi:10.1126/sciadv.adk7535 ]
- Allophycocyanin subunit beta-18 (18 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803)
- Complex of phycobilisome from synechocystis pcc 6803 bound to ocp (Complex from Synechocystis sp. (strain PCC 6803 / Kazusa))
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Translation initiation factor if-2 (12 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin subunit alpha-b (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycobilisome rod-core linker polypeptide cpcg (28 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 [ Pubmed: 38578996 DOI: doi:10.1126/sciadv.adk7535 ]
- Allophycocyanin beta chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Water (18 Da, Ligand)
- Phycobiliprotein apce (100 kDa, Protein from Synechocystis sp. PCC 6803)
- Orange carotenoid-binding protein (34 kDa, Protein from Synechocystis sp. PCC 6803)
- Phycobilisome bound to ocp (Complex from Synechocystis sp. PCC 6803)
- Phycocyanobilin (588 Da, Ligand)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Allophycocyanin alpha chain (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Phycobilisome rod-core linker polypeptide cpcg (28 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 [ Pubmed: 38578996 DOI: doi:10.1126/sciadv.adk7535 ]
- Phycobilisome 8.9 kda linker polypeptide, phycocyanin-associated, rod (9 kDa, Protein from Synechocystis sp. PCC 6803)
- Water (18 Da, Ligand)
- Phycobilisome bound to ocp (Complex from Synechocystis sp. PCC 6803)
- Phycocyanobilin (588 Da, Ligand)
- C-phycocyanin beta subunit (18 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 1 (32 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 rod-core linker polypeptide cpcg (28 kDa, Protein from Synechocystis sp. PCC 6803)
Cryo-EM structure of the CRT-LESS RC-LH core complex from roseiflexus castenholzii
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8iun
Q-score: 0.613
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Cardiolipin (1 kDa, Ligand)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- Crt-less rc-lh core complex (Complex from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Bacteriochlorophyll a (911 Da, Ligand)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- Unknown ligand (691 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Heme c (618 Da, Ligand)
- Gamma-carotene (536 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
Cryo-EM structure of the RC-LH core complex from roseiflexus castenholzii
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8iug
Q-score: 0.622
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Unknown ligand (Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- Rc-lh core complex (Complex from Roseiflexus castenholzii)
- Manganese (ii) ion (54 Da, Ligand)
- Tmx polypeptide (3 kDa, Protein from Roseiflexus castenholzii)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Heme c (618 Da, Ligand)
- [(2~{r},3~{s},4~{s},5~{r},6~{r})-6-[(6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate (941 Da, Ligand)
- Gamma-carotene (536 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
In situ double-PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum.
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- In situ double-pbs-psii-psi-lhcs megacomplex from porphyridium purpureum. (Cell from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Carsp2 (15 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein of lhcii type iii, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i subunit o (9 kDa, Protein from Porphyridium purpureum)
- Ferredoxin (10 kDa, Protein from Porphyridium purpureum)
- Carsp1 (24 kDa, Protein from Porphyridium purpureum)
- Cytochrome c6 (8 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein t (3 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit psak (6 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein d1 (39 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein l (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Redcap (19 kDa, Protein from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Iron/sulfur cluster (351 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)
- Phycourobilin (590 Da, Ligand)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp43 reaction center protein (52 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center x protein (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Oxygen-evolving enhancer protein (30 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Porphyridium purpureum)
- Fucoxanthin-chlorophyll a-c binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- (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)
- Phylloquinone (450 Da, Ligand)
- Psii_pbs31 domain-containing protein (22 kDa, Protein from Porphyridium purpureum)
- Fe (iii) ion (55 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Lr6 (46 kDa, Protein from Porphyridium purpureum)
- Psar (12 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Porphyridium purpureum)
- Lrh (20 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Porphyridium purpureum)
- Linker4 (11 kDa, Protein from Porphyridium purpureum)
- Psbm (10 kDa, Protein from Porphyridium purpureum)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (37 kDa, Protein from Porphyridium purpureum)
- Psb34 (2 kDa, Protein from Porphyridium purpureum)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein y (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein k (5 kDa, Protein from Porphyridium purpureum)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Phycoerythrobilin (588 Da, Ligand)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Porphyridium purpureum)
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- Psbw (3 kDa, Protein from Porphyridium purpureum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lpp1 (10 kDa, Protein from Porphyridium purpureum)
- Ps ii complex 12 kda extrinsic protein (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome c550 (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein h (7 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- Lps1 (5 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Porphyridium purpureum)
- Photosystem ii d2 protein (39 kDa, Protein from Porphyridium purpureum)
- Cnt (10 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein j (3 kDa, Protein from Porphyridium purpureum)
- Psbq' (22 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (27 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit beta (5 kDa, Protein from Porphyridium purpureum)
- Psab (82 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
In situ single-PBS-PSII-PSI-LHCs megacomplex.
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7y5e
Q-score: 0.318
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (46 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein of lhcii type iii, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i subunit o (9 kDa, Protein from Porphyridium purpureum)
- Ferredoxin (10 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein t (3 kDa, Protein from Porphyridium purpureum)
- Psar (8 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit psak (6 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein d1 (39 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Carsps1 (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Redcap (19 kDa, Protein from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Iron/sulfur cluster (351 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)
- Phycourobilin (590 Da, Ligand)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- Photosystem ii cp43 reaction center protein (52 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center x protein (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Oxygen-evolving enhancer protein (30 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Cytochrome c6 (11 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Porphyridium purpureum)
- Psaa (83 kDa, Protein from Porphyridium purpureum)
- Fucoxanthin-chlorophyll a-c binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- (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)
- Phylloquinone (450 Da, Ligand)
- Psii_pbs31 domain-containing protein (22 kDa, Protein from Porphyridium purpureum)
- Fe (iii) ion (55 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- In situ single-pbs-psii-psi-lhcs megacomplex (Cell from Porphyridium purpureum)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Porphyridium purpureum)
- Lrh (20 kDa, Protein from Porphyridium purpureum)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Porphyridium purpureum)
- Psbm (10 kDa, Protein from Porphyridium purpureum)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Porphyridium purpureum)
- Psb34 (2 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (37 kDa, Protein from Porphyridium purpureum)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein y (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein k (5 kDa, Protein from Porphyridium purpureum)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Phycoerythrobilin (588 Da, Ligand)
- Linker4 (14 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (32 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- Psbw (3 kDa, Protein from Porphyridium purpureum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lpp1 (10 kDa, Protein from Porphyridium purpureum)
- Ps ii complex 12 kda extrinsic protein (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome c550 (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein h (7 kDa, Protein from Porphyridium purpureum)
- Carsp2 (36 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Porphyridium purpureum)
- Lps1 (5 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Porphyridium purpureum)
- Cnt (10 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein j (3 kDa, Protein from Porphyridium purpureum)
- Psbq' (22 kDa, Protein from Porphyridium purpureum)
- Psbl (4 kDa, Protein from Porphyridium purpureum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit beta (5 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
PBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum.
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (36 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (45 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Carsps2 (35 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Phycoerythrobilin (588 Da, Ligand)
- Linker4 (14 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (32 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- In situ pbs from porphyridium purpureum (Cell from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Carsps1 (28 kDa, Protein from Porphyridium purpureum)
- Phycourobilin (590 Da, Ligand)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)