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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) [ Pubmed: 38411333 DOI: doi:10.1111/jipb.13628 ]
- Reaction center protein l chain (31 kDa, Protein from Halorhodospira halochloris)
- Beta subunit of light-harvesting 1 (9 kDa, Protein from Halorhodospira halochloris)
- Antenna complex alpha/beta subunit domain-containing protein (12 kDa, Protein from Halorhodospira halochloris)
- Fe (iii) ion (55 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Gamma subunit of light-harvesting 1 (3 kDa, Protein from Halorhodospira halochloris)
- Ubiquinone-8 (727 Da, Ligand)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Halorhodospira halochloris)
- Reaction center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Lycopene (536 Da, Ligand)
- Photosynthetic reaction center h subunit (31 kDa, Protein from Halorhodospira halochloris)
- Heme c (618 Da, Ligand)
- Trans-geranyl bacteriochlorophyll b (907 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Halorhodospira halochloris)
- Cardiolipin (1 kDa, Ligand)
- Trans-geranyl bacteriopheophytin b (885 Da, Ligand)
- Light-harvesting lhi (7 kDa, Protein from Halorhodospira halochloris)
- Trans-geranyl 8-vinyl-bacteriochlorophyll b (907 Da, Ligand)
- Rc-lh core complex (Complex from Halorhodospira halochloris)
- Antenna complex alpha/beta subunit domain-containing protein (7 kDa, Protein from Halorhodospira halochloris)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Unknown ligand (909 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Reactin center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 2,000lux
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8j5p
Q-score: 0.562
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ DOI: doi:10.7554/eLife.88951 Pubmed: 37737710 ]
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Bacteriopheophytin b (887 Da, Ligand)
- The native rc-lh complex at 2,000lux (Complex from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Fe (iii) ion (55 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Rba sphaeroides WT RC-LH1 monomer
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 7vny
Q-score: 0.633
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ DOI: doi:10.1038/s41467-022-29563-3 Pubmed: 35418573 ]
- Rhodobacter sphaeroides wt rc-lh1 monomer (Complex from Rhodobacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Rsp_7571 protein-y pufy (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 dimer type-1
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 7va9
Q-score: 0.517
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ DOI: doi:10.1038/s41467-022-29563-3 Pubmed: 35418573 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides pufy-ko rc-lh1 dimer type-1 (Complex from Rhodobacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7vot
Q-score: 0.542
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ DOI: doi:10.1038/s41467-022-29563-3 Pubmed: 35418573 ]
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Rsp_7571 protein-y pufy (5 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Bacteriopheophytin b (887 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Intrinsic membrane protein pufx (9 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- The dimeric photosynthetic rc-lh1 supercomplex in class2 (Complex from Cereibacter sphaeroides 2.4.1)
- Reaction center protein h chain (28 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
Reaction centre light harvesting complex 1 from Blc. virids
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 6et5
Q-score: 0.469
Qian P, Siebert CA, Wang P, Canniffe DP, Hunter CN
Nature (2018) 556 pp. 203-208 [ Pubmed: 29618818 DOI: doi:10.1038/s41586-018-0014-5 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Bacteriochlorophyll b (909 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Rhodopseudomonas viridis)
- All-trans-1,2-dihydroneurosporene (540 Da, Ligand)
- 15-cis-1,2-dihydroneurosporene (540 Da, Ligand)
- Light-harvesting protein b-1015 gamma chain (2 kDa, Protein from Rhodopseudomonas viridis)
- Menaquinone-9 (785 Da, Ligand)
- Reaction center protein l chain (30 kDa, Protein from Rhodopseudomonas viridis)
- Bacteriopheophytin b (887 Da, Ligand)
- Light-harvesting protein b-1015 beta chain (6 kDa, Protein from Rhodopseudomonas viridis)
- Fe (iii) ion (55 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Reaction centre-light harvesting complex 1 (rc-lh1) (414 kDa, Complex from Blastochloris viridis)
- Light-harvesting protein b-1015 alpha chain (6 kDa, Protein from Rhodopseudomonas viridis)
- Sulfate ion (96 Da, Ligand)
- Reaction center protein m chain (35 kDa, Protein from Rhodopseudomonas viridis)
- Ubiquinone-9 (795 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (37 kDa, Protein from Rhodopseudomonas viridis)