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)
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 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 ]
- 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)
- 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)
- The carotenoid-depleted rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Protoporphyrin ix containing fe (616 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)
- 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)
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 ]
- 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)
- 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)
- 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)
- Bacteriopheophytin b (887 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)
- The native rc-lh complex at 2,000lux (Complex from Roseiflexus castenholzii DSM 13941)
- Fe (iii) ion (55 Da, Ligand)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Resolution: 3.99 Å
EM Method: Single-particle
Fitted PDBs: 7suk
Q-score: 0.314
Zhao Y, Rai J, Xu C, He H, Li H
Commun Biol (2022) 5 pp. 523-523 [ DOI: doi:10.1038/s42003-022-03500-y Pubmed: 35650250 ]
- Periodic tryptophan protein 2 (96 kDa, Protein from Saccharomyces cerevisiae)
- Rrna-processing protein fcf1 (21 kDa, Protein from Saccharomyces cerevisiae)
- Ribosome biogenesis protein utp30 (28 kDa, Protein from Saccharomyces cerevisiae)
- Net1-associated nuclear protein 1 (100 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s16-a (13 kDa, Protein from Saccharomyces cerevisiae)
- Ribonucloprotein (13 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 15 (57 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Saccharomyces cerevisiae)
- Pre-rrna-processing protein pno1 (20 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal rna small subunit methyltransferase nep1 (26 kDa, Protein from Saccharomyces cerevisiae)
- Ribosome biogenesis protein bms1 (127 kDa, Protein from Saccharomyces cerevisiae)
- 5' ets (225 kDa, RNA from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 4 (84 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s5 (23 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 18s pre-rrna (582 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (14 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar ribonucleoprotein protein lcp5 (40 kDa, Protein from Saccharomyces cerevisiae)
- Something about silencing protein 10 (20 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 7 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rrna-processing protein fcf2 (20 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 20 (278 kDa, Protein from Saccharomyces cerevisiae)
- Structure of bfr2-lcp5 complex observed in the small subunit processome isolated from r2tp-depleted yeast cells (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (25 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 21 (102 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (11 kDa, Protein from Saccharomyces cerevisiae)
- Rrp9 isoform 1 (52 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (25 kDa, Protein from Saccharomyces cerevisiae)
- Protein faf1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Nucleolar protein 58 (47 kDa, Protein from Saccharomyces cerevisiae)
- Rrna 2'-o-methyltransferase fibrillarin (27 kDa, Protein from Saccharomyces cerevisiae)
- Krr1 small subunit processome component (20 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein mpp10 (28 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 14 (21 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 13 (90 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 12 (104 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 9 (13 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Essential nuclear protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 11 (29 kDa, Protein from Saccharomyces cerevisiae)
- Nucleolar complex protein 14 (89 kDa, Protein from Saccharomyces cerevisiae)
- Rrna biogenesis protein rrp5 (30 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s18-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Rna 3'-terminal phosphate cyclase-like protein (39 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 10 (49 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 6 (46 kDa, Protein from Saccharomyces cerevisiae)
- Ribosome biogenesis protein enp2 (41 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal rna-processing protein 7 (21 kDa, Protein from Saccharomyces cerevisiae)
- Nucleolar protein 56 (45 kDa, Protein from Saccharomyces cerevisiae)
- Bud site selection protein 21 (7 kDa, Protein from Saccharomyces cerevisiae)
- U3 snorna (106 kDa, RNA from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 22 (130 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae)
- Nucleolar complex protein 4 (59 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 8 (77 kDa, Protein from Saccharomyces cerevisiae)
- Protein bfr2 (61 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-b (11 kDa, Protein from Saccharomyces cerevisiae)
- Rna cytidine acetyltransferase (104 kDa, Protein from Saccharomyces cerevisiae)
- Protein sof1 (53 kDa, Protein from Saccharomyces cerevisiae)
- U3 small nucleolar rna-associated protein 5 (62 kDa, Protein from Saccharomyces cerevisiae)
- Regulator of rdna transcription protein 14 (10 kDa, Protein from Saccharomyces cerevisiae)
Structure of the Lactococcus lactis Csm CTR_4:3 CRISPR-Cas Complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6xn3
Q-score: 0.467
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 csm2 (15 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr-associated protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Lactococcus lactis csm crispr-cas ntr complex (Complex 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-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)
Structure of the Lactococcus lactis Csm CTR_3:2 CRISPR-Cas Complex
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 6xn4
Q-score: 0.414
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 csm2 (15 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr-associated protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Lactococcus lactis csm crispr-cas ctr_3:2 complex (Complex from Lactococcus lactis subsp. lactis)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Target rna (9 kDa, RNA 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)
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)