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Qian P, Gardiner AT, Šímová I, Naydenova K, Croll TI, Jackson PJ, Nupur N, Kloz M, Čubáková P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hájek J, Agirre J, Siebert CA, Bína D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polívka T, Hunter CN, Koblížek M
Sci Adv (2022) 8 [ DOI: 10.1126/sciadv.abk3139 Pubmed: 35171663 ]
Image sets:
Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 7o0u
Q-score: 0.629
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- Rc-dlh model_1a (800 kDa, Complex from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7o0v
Q-score: 0.62
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Light-harvesting protein b:885 subunit beta (4 kDa, Protein from Gemmatimonas phototrophica)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh (model_2a) (800 kDa, Complex from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
Cryo-EM structure of the RC-dLH complex (model_1b) from Gemmatimonas phototrophica at 2.47 A
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 7o0w
Q-score: 0.624
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Rc-dlh model_1b (800 kDa, Complex from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 7o0x
Q-score: 0.629
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7pqd
Q-score: 0.582
Qian P, Croll TI, Hitchcock A, Jackson PJ, Salisbury JH, Castro-Hartmann P, Sader K, Swainsbury DJK, Hunter CN
Biochem J (2021) 478 pp. 3923-3937 [ DOI: doi:10.1042/BCJ20210696 Pubmed: 34622934 ]
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rc-l (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lh1-alpha (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Pufx (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rc-h (26 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-1 (250 Da, Ligand)
- Pufy (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Lh1-beta (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- 3,4-dihydrospheroidene (570 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Light harvesting core complex (Complex from Cereibacter sphaeroides 2.4.1)
- Pufz (3 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Water (18 Da, Ligand)
Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7pil
Q-score: 0.64
Qian P, Swainsbury DJK, Croll TI, Salisbury JH, Martin EC, Jackson PJ, Hitchcock A, Castro-Hartmann P, Sader K, Hunter CN
Biochem J (2021) 478 pp. 3775-3790 [ Pubmed: 34590677 DOI: doi:10.1042/BCJ20210631 ]
- Intrinsic membrane protein pufx (5 kDa, Protein from Cereibacter sphaeroides)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Rc-y (5 kDa, Protein from Cereibacter sphaeroides)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Reaction center protein h chain (26 kDa, Protein from Cereibacter sphaeroides)
- Ubiquinone-1 (250 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Light harvesting complex (Complex from Cereibacter sphaeroides 2.4.1)
- Water (18 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
- Light-harvesting protein b-875 beta chain (4 kDa, Protein from Cereibacter sphaeroides)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides)
Movies of a heptameric light-harvesting 2 complex from the marine purple bacterium Mch. purpuratum
Gardiner AT, Naydenova K, Castro-Hartmann P, Nguyen-Phan TC, Russo CJ, Sader K, Hunter CN, Cogdell RJ, Qian P
Sci Adv (2021) 7 [ DOI: 10.1126/sciadv.abe4650 Pubmed: 33579696 ]
Image sets:
LH2 complex from Marichromatium purpuratum
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 6zxa
Q-score: 0.675
Gardiner AT, Naydenova K, Castro-Hartmann P, Nguyen-Phan TC, Russo CJ, Sader K, Hunter CN, Cogdell RJ, Qian P
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abe4650 Pubmed: 33579696 ]
- Lhc domain-containing protein (8 kDa, Protein from Marichromatium purpuratum 984)
- Bacteriochlorophyll a (911 Da, Ligand)
- All-trans okenone (578 Da, Ligand)
- 9-cis-okenone (578 Da, Ligand)
- Light harvesting complex 2 (lh2) (110 kDa, Complex from Marichromatium purpuratum)
- Light-harvesting protein b:800-850 subunit beta (5 kDa, Protein from Marichromatium purpuratum 984)
Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Löwe J, Barford D, Russo CJ
Proc Natl Acad Sci U S A (2021) 118 [ Pubmed: 33526596 DOI: 10.1073/pnas.2021946118 ]
Image sets: