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Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7yml
Q-score: 0.613
Tani K, Kanno R, Ji XC, Satoh I, Kobayashi Y, Hall M, Yu LJ, Kimura Y, Mizoguchi A, Humbel BM, Madigan MT, Wang-Otomo ZY
Nat Commun (2023) 14 pp. 846-846 [ DOI: doi:10.1038/s41467-023-36460-w Pubmed: 36792596 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Myristic acid (228 Da, Ligand)
- Photosynthetic reaction center pufx protein (8 kDa, Protein from Rhodobacter capsulatus)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (6 kDa, Protein from Rhodobacter capsulatus)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Rhodobacter capsulatus)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodobacter capsulatus (Complex from Rhodobacter capsulatus)
- Ubiquinone-10 (863 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Water (18 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Light-harvesting protein b-870 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Resolution: 2.589 Å
EM Method: Single-particle
Fitted PDBs: 8b64
Q-score: 0.639
Bracun L, Yamagata A, Christianson BM, Shirouzu M, Liu LN
Structure (2023) 31 pp. 318- [ DOI: doi:10.1016/j.str.2023.01.006 Pubmed: 36738736 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Intrinsic membrane protein pufx (8 kDa, Protein from Rhodobacter capsulatus)
- Rc-lh1-pufx photosynthetic core complex from rba. capsulatus (Complex from Rhodobacter capsulatus)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- Lh1 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Rhodobacter capsulatus)
- Spheroidene (568 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (6 kDa, Protein from Rhodobacter capsulatus)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
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 ]
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Rsp_7571 protein-y pufy (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- Rhodobacter sphaeroides wt rc-lh1 monomer (Complex from Rhodobacter sphaeroides 2.4.1)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 beta chain (5 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 ]
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- 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 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 dimer type-2
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7vb9
Q-score: 0.456
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 ]
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides pufy-ko rc-lh1 dimer type-2 (Complex from Rhodobacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 monomer
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 7vnm
Q-score: 0.591
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 ]
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides pufy-ko rc-lh1 monomer (Complex from Rhodobacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufX-KO RC-LH1
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7voy
Q-score: 0.372
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)
- Bacteriopheophytin a (889 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Speroidenone (594 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Rhodobacter sphaeroides pufx-ko rc-lh1 (Complex from Rhodobacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 7vor
Q-score: 0.573
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 ]
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Spheroidene (568 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- The dimeric photosynthetic rc-lh1 supercomplex in class1 (Complex from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides)
- Fe (ii) ion (55 Da, Ligand)
- Rsp_7571 protein-y pufy (5 kDa, Protein from Cereibacter sphaeroides)
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 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Cardiolipin (1 kDa, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- 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 alpha chain (6 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Rsp_7571 protein-y pufy (5 kDa, Protein from Rhodobacter sphaeroides 2.4.1)
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 7vy2
Q-score: 0.534
Tani K, Kanno R, Kikuchi R, Kawamura S, Nagashima KVP, Hall M, Takahashi A, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY
Nat Commun (2022) 13 pp. 1904-1904 [ Pubmed: 35393413 DOI: doi:10.1038/s41467-022-29453-8 ]
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodobacter sphaeroides dimer (Complex from Rhodobacter sphaeroides f. sp. denitrificans)
- Pufx (8 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Spheroidene (568 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Rhodobacter sphaeroides dimeric lh1-rc complex (Complex from Rhodobacter sphaeroides f. sp. denitrificans)
- Ubiquinone-10 (863 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Antenna pigment protein beta chain (5 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosynthetic reaction center l subunit (31 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Antenna pigment protein alpha chain (6 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Photosynthetic reaction center subunit h (28 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Protein-u (5 kDa, Protein from Rhodobacter sphaeroides f. sp. denitrificans)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)