human NaS1 intermediate state 2
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8y5w
Q-score: 0.579
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Membrane sodium anion transproter 2 (Complex from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
human NaS1 intermediate state 3
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8y5x
Q-score: 0.484
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Membrane sodium anion transproter 3 (Cellular component from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Sulfate ion (96 Da, Ligand)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8y5y
Q-score: 0.443
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Membrane sodium anion transproter out (Complex from Homo sapiens)
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8y5z
Q-score: 0.474
Chen X, Zhang Y, Yin J, Liu C, Xie M, Wang Y, Chen M, Zhang R, Yuan X, Li D, Chen X, Gao X, Cai G, Zhang S, Zhou B, Yang M
Sci Adv (2024) 10 pp. eado6778-eado6778 [ Pubmed: 39576865 DOI: doi:10.1126/sciadv.ado6778 ]
- Solute carrier family 13 member 1 (66 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Membrane sodium anion transproter in (Complex from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8k9e
Q-score: 0.548
Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X
Plant Cell (2024) [ Pubmed: 38299372 DOI: doi:10.1093/plcell/koae029 ]
- Uncharacterized protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Heme c (618 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- [(2s)-2-octadecanoyloxypropyl] octadecanoate (609 Da, Ligand)
- Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
- Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8k9f
Q-score: 0.527
Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X
Plant Cell (2024) [ Pubmed: 38299372 DOI: doi:10.1093/plcell/koae029 ]
- Heme c (618 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Magnesium ion (24 Da, Ligand)
- Hypothetical protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
- Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8x2j
Q-score: 0.561
Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X
Plant Cell (2024) [ Pubmed: 38299372 DOI: doi:10.1093/plcell/koae029 ]
- 2-heptyl-4-hydroxy quinoline n-oxide (259 Da, Ligand)
- Uncharacterized protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Heme c (618 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
- Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 10,000 lux
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8hju
Q-score: 0.603
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Diacyl glycerol (625 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The native rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Cryo-EM structure of carotenoid-depleted RC-LH complex from Roseiflexus castenholzii at 10,000 lux
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hjv
Q-score: 0.478
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The carotenoid-depleted rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j5o
Q-score: 0.606
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The native rc-lh complex at 100lux (Complex from Roseiflexus castenholzii DSM 13941)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriopheophytin a (889 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)