Cryo-EM of helical fibers formed by two peptides Pyn-K6 and Pyn-(EY)3
Resolution: 3.3 Å
EM Method: Helical reconstruction
Fitted PDBs: 9d70
Q-score: 0.39
Qiao Y, Zia A, Wu G, Liu Z, Guo J, Chu M, He H, Wang F, Xu B
J Am Chem Soc (2025) 147 pp. 2978-2983 [ Pubmed: 39808585 DOI: doi:10.1021/jacs.4c12150 ]
- (pyren-1-yl)acetic acid (260 Da, Ligand)
- Pyr-ey3 (1 kDa, Protein from synthetic construct)
- Pyr-k6 (1 kDa, Protein from synthetic construct)
- Pyn-k6 + pyn-ey3 fiber (Complex from synthetic construct)
Cryo-EM structure of the active Lactococcus lactis Csm bound to target in post-cleavage stage
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 9ash
Q-score: 0.56
Goswami HN, Ahmadizadeh F, Wang B, Addo-Yobo D, Zhao Y, Whittington AC, He H, Terns MP, Li H
Nucleic Acids Res (2024) 52 pp. 10619-10629 [ DOI: doi:10.1093/nar/gkae603 Pubmed: 38989619 ]
- Crispr-associated protein csm4 (33 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (87 kDa, Protein from Lactococcus lactis subsp. lactis)
- Target rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Atp bound lactococcus lactis csm crispr-cas complex with stable cas10 (Complex from Lactococcus lactis subsp. lactis)
- Water (18 Da, Ligand)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Rna (5'-d(*(atp))-r(p*ap*a)-3') (1 kDa, RNA from Lactococcus lactis subsp. lactis)
- Magnesium ion (24 Da, Ligand)
- Crispr system cms protein csm2 (17 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Cryo-EM structure of the active Lactococcus lactis Csm bound to target in pre-cleavage stage
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 9asi
Q-score: 0.467
Goswami HN, Ahmadizadeh F, Wang B, Addo-Yobo D, Zhao Y, Whittington AC, He H, Terns MP, Li H
Nucleic Acids Res (2024) 52 pp. 10619-10629 [ DOI: doi:10.1093/nar/gkae603 Pubmed: 38989619 ]
- Crispr-associated protein csm4 (33 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Target rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Lactococcus lactis csm crispr-cas complex, atp bound and cas10 flexible (Complex from Lactococcus lactis subsp. lactis)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (87 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Adenosine monophosphate (347 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Crispr system cms protein csm2 (17 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Adenosine-5'-triphosphate (507 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) [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]
- [(2s)-2-octadecanoyloxypropyl] octadecanoate (609 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- Uncharacterized protein (12 kDa, Protein 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))
- Cytochrome c domain-containing protein (23 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))
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Fe3-s4 cluster (295 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Heme c (618 Da, Ligand)
- Polysulphide reductase nrfd (55 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))
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Cytochrome c7-like domain-containing protein (25 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) [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- 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))
- Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Magnesium ion (24 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))
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Fe3-s4 cluster (295 Da, Ligand)
- Hypothetical protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Iron/sulfur cluster (351 Da, Ligand)
- Heme c (618 Da, Ligand)
- Polysulphide reductase nrfd (55 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))
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Cytochrome c7-like domain-containing protein (25 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) [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- Uncharacterized protein (12 kDa, Protein 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))
- Cytochrome c domain-containing protein (23 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))
- 2-heptyl-4-hydroxy quinoline n-oxide (259 Da, Ligand)
- Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Fe3-s4 cluster (295 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Heme c (618 Da, Ligand)
- Polysulphide reductase nrfd (55 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))
- Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
- Cytochrome c7-like domain-containing protein (25 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 ]
- 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)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriopheophytin a (889 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- The native rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Protoporphyrin ix containing fe (616 Da, Ligand)
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 ]
- The carotenoid-depleted rc-lh complex (Complex 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)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriopheophytin a (889 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- (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)
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 ]
- 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)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The native rc-lh complex at 100lux (Complex from Roseiflexus castenholzii DSM 13941)
- Fe (iii) ion (55 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
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 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- 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)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin b (887 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Fe (iii) ion (55 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- The native rc-lh complex at 2,000lux (Complex from Roseiflexus castenholzii DSM 13941)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)