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 ]
- Magnesium ion (24 Da, Ligand)
- Crispr-associated protein csm4 (33 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)
- Water (18 Da, Ligand)
- Crispr system cms protein csm2 (17 kDa, Protein from Lactococcus lactis subsp. lactis)
- Rna (5'-d(*(atp))-r(p*ap*a)-3') (1 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)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Target rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Atp bound lactococcus lactis csm crispr-cas complex with stable cas10 (Complex from Lactococcus lactis subsp. lactis)
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 ]
- Magnesium ion (24 Da, Ligand)
- Lactococcus lactis csm crispr-cas complex, atp bound and cas10 flexible (Complex from Lactococcus lactis subsp. lactis)
- Crispr-associated protein csm4 (33 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)
- Adenosine monophosphate (347 Da, Ligand)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (87 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms protein csm2 (17 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)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
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) 36 pp. 4212-4233 [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]
- Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
- Hypothetical protein (12 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)
- Alternative complex iii (Complex 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))
- Fe-s-cluster-containing hydrogenase components 1-like protein (113 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))
- Heme c (618 Da, Ligand)
- Magnesium ion (24 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))
- Fe3-s4 cluster (295 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- 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))
- Iron/sulfur cluster (351 Da, Ligand)
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) 36 pp. 4212-4233 [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]
- Polysulphide reductase nrfd (55 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)
- Alternative complex iii (Complex 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))
- Fe-s-cluster-containing hydrogenase components 1-like protein (113 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))
- Heme c (618 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))
- Fe3-s4 cluster (295 Da, Ligand)
- 2-heptyl-4-hydroxy quinoline n-oxide (259 Da, Ligand)
- [(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
- 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))
- Iron/sulfur cluster (351 Da, Ligand)
- Uncharacterized protein (12 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 ]
- 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)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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 z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- 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)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Fe (iii) ion (55 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 ]
- 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)
- The native rc-lh complex at 100lux (Complex from Roseiflexus castenholzii DSM 13941)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit z (6 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)
- 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)
- Fe (iii) ion (55 Da, Ligand)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Resolution: 2.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 8fof
Q-score: 0.672
Guo J, Wang F, Huang Y, He H, Tan W, Yi M, Egelman EH, Xu B
Nat Nanotechnol (2023) 18 pp. 1094-1104 [ Pubmed: 37217766 DOI: doi:10.1038/s41565-023-01401-7 ]
- Bp-ffsy (Complex from synthetic construct)
- Bp-ffsy (742 Da, Protein from synthetic construct)
Structure of the Lactococcus lactis Csm Apo- CRISPR-Cas Complex
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 6xn5
Q-score: 0.486
Sridhara S, Rai J, Whyms C, Goswami H, He H, Woodside W, Terns MP, Li H
Commun Biol (2022) 5 pp. 279-279 [ Pubmed: 35351985 DOI: doi:10.1038/s42003-022-03187-1 ]
- Crispr-associated protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr rna (10 kDa, RNA from Lactococcus lactis subsp. lactis)
- Lactococcus lactis csm crispr-cas apo complex (Complex from Lactococcus lactis subsp. lactis)
- Crispr-associated protein csm4 (33 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr-associated protein csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr-associated protein cas10 (87 kDa, Protein from Lactococcus lactis subsp. lactis)
Cryo-EM structure of DgpB-C at 2.85 angstrom resolution
Mori T, Kumano T, He H, Watanabe S, Senda M, Moriya T, Adachi N, Hori S, Terashita Y, Kawasaki M, Hashimoto Y, Awakawa T, Senda T, Abe I, Kobayashi M
Nat Commun (2021) 12 pp. 6294-6294 [ Pubmed: 34728636 DOI: doi:10.1038/s41467-021-26585-1 ]
- Dgpb-c (250 kDa, Complex from human intestinal bacterium PUE)
Cryo-EM structure of DfgA-B at 2.54 angstrom resolution
Mori T, Kumano T, He H, Watanabe S, Senda M, Moriya T, Adachi N, Hori S, Terashita Y, Kawasaki M, Hashimoto Y, Awakawa T, Senda T, Abe I, Kobayashi M
Nat Commun (2021) 12 pp. 6294-6294 [ Pubmed: 34728636 DOI: doi:10.1038/s41467-021-26585-1 ]
- Dfgb (Protein from [Eubacterium] cellulosolvens)
- Dfga (Protein from [Eubacterium] cellulosolvens)
- Dfga-b (250 kDa, Complex from Eubacterium cellulosolvens)