Cryo-EM structure of Lactobacillus casei DdmE bound with guide and target
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 9iw3
Q-score: 0.438
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ Pubmed: 39448873 DOI: doi:10.1038/s41422-024-01042-y ]
- Dna (25-mer) (7 kDa, DNA from Lacticaseibacillus)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*tp*tp*gp*ap*tp*ap*cp*gp*ap*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Lactobacillus casei ddme bound with guide and target (Complex from Lacticaseibacillus)
- Dna (5'-d(p*tp*gp*ap*cp*gp*gp*cp*tp*cp*tp*ap*ap*tp*cp*t)-3') (4 kDa, DNA from Lacticaseibacillus)
- Ddme (83 kDa, Protein from Lacticaseibacillus)
Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 9ix4
Q-score: 0.483
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ Pubmed: 39448873 DOI: doi:10.1038/s41422-024-01042-y ]
- Dna (5'-d(p*tp*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (3 kDa, DNA from Lacticaseibacillus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ddmd (137 kDa, Protein from Lacticaseibacillus)
- Lactobacillus casei ddmd bound with dna substrate (Complex from Lacticaseibacillus)
- Dna (5'-d(p*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA from Lacticaseibacillus)
Cryo-EM structure of Lactobacillus casei DdmDE bound with DNA
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 9ixm
Q-score: 0.464
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ Pubmed: 39448873 DOI: doi:10.1038/s41422-024-01042-y ]
- Ddmd (137 kDa, Protein from Lacticaseibacillus)
- Dna (30-mer) (9 kDa, DNA from Lacticaseibacillus)
- Magnesium ion (24 Da, Ligand)
- Dna (30-mer) (9 kDa, DNA from Lacticaseibacillus)
- Ddme (83 kDa, Protein from Lacticaseibacillus)
- Dna (5'-d(p*tp*gp*ap*cp*gp*gp*cp*tp*cp*tp*ap*ap*tp*cp*t)-3') (4 kDa, DNA from Lacticaseibacillus)
- Lactobacillus casei ddmde bound with dna (Complex from Lacticaseibacillus)
The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2025) 387 pp. eadr0393-eadr0393 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Adenosine deaminase domain-containing protein (69 kDa, Protein from Limisphaera ngatamarikiensis)
- Rna (5'-r(p*ap*ap*ap*ap*ap*a)-3') (1 kDa, RNA from Limisphaera ngatamarikiensis)
- Caad:ca6:atp 6:3:6 (Complex from Limisphaera ngatamarikiensis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
The structure of type III CRISPR-associated deaminase in complex cA4
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2025) 387 pp. eadr0393-eadr0393 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Adenosine deaminase domain-containing protein (70 kDa, Protein from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- 3'-o-[(r)-{[(2s,3as,4s,6s,6as)-6-(6-amino-9h-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2h-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine (658 Da, Ligand)
PSI-FCPI-L in Thalassiosira pseudonana
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8zeh
Q-score: 0.566
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Tp-lhcr18 (16 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-PSI-FCPI-S in Thalassiosira pseudonana
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8zet
Q-score: 0.485
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Tp-psi-fcpi-s (Complex from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 Da, Ligand)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
The structure of type III CRISPR-associated deaminase in complex 2cA6 and 2ATP, partial activated
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2025) 387 pp. eadr0393-eadr0393 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Zinc ion (65 Da, Ligand)
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- Adenosine deaminase domain-containing protein (70 kDa, Protein from Limisphaera ngatamarikiensis)
- Rna (5'-r(p*ap*ap*ap*ap*ap*a)-3') (1 kDa, RNA from Limisphaera ngatamarikiensis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Cryo-EM structure of human urea transporter A2.
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8xdb
Q-score: 0.515
Huang SM, Huang ZZ, Liu L, Xiong MY, Zhang C, Cai BY, Wang MW, Cai K, Jia YL, Wang JL, Zhang MH, Xie YH, Li M, Zhang H, Weng CH, Wen X, Li Z, Sun Y, Yi F, Yang Z, Xiao P, Yang F, Yu X, Tie L, Yang BX, Sun JP
Nat Commun (2024) 15 pp. 10226-10226 [ Pubmed: 39587082 DOI: doi:10.1038/s41467-024-54305-y ]
Cryo-EM structure of human urea transporter A2.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8xdc
Q-score: 0.562
Huang SM, Huang ZZ, Liu L, Xiong MY, Zhang C, Cai BY, Wang MW, Cai K, Jia YL, Wang JL, Zhang MH, Xie YH, Li M, Zhang H, Weng CH, Wen X, Li Z, Sun Y, Yi F, Yang Z, Xiao P, Yang F, Yu X, Tie L, Yang BX, Sun JP
Nat Commun (2024) 15 pp. 10226-10226 [ Pubmed: 39587082 DOI: doi:10.1038/s41467-024-54305-y ]