Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 monomer state
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8vh4
Q-score: 0.333
Li X, Zhu H, Huang BT, Li X, Kim H, Tan H, Zhang Y, Choi I, Peng J, Xu P, Sun J, Yue Z
Nat Commun (2024) 15 pp. 8434-8434 [ Pubmed: 39343966 DOI: doi:10.1038/s41467-024-52723-6 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Rab12-lrrk2 (Complex from Homo sapiens)
- Leucine-rich repeat serine/threonine-protein kinase 2 (286 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Ras-related protein rab-12 (20 kDa, Protein from Homo sapiens)
Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 dimer state
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8vh5
Q-score: 0.248
Li X, Zhu H, Huang BT, Li X, Kim H, Tan H, Zhang Y, Choi I, Peng J, Xu P, Sun J, Yue Z
Nat Commun (2024) 15 pp. 8434-8434 [ Pubmed: 39343966 DOI: doi:10.1038/s41467-024-52723-6 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Rab12-lrrk2 (Complex from Homo sapiens)
- Leucine-rich repeat serine/threonine-protein kinase 2 (286 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Ras-related protein rab-12 (20 kDa, Protein from Homo sapiens)
Cryo-EM structure of Cas8-HNH system at full R-loop state
Resolution: 2.51 Å
EM Method: Single-particle
Fitted PDBs: 8z0k
Q-score: 0.551
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Hypothetical protein j6n51_11000 (28 kDa, Protein from Selenomonas sp.)
- Cryo-em structure of cas8-hnh system at full r-loop state (Complex from Selenomonas sp.)
- Rna (69-mer) (22 kDa, RNA from Selenomonas sp.)
- Type i-f crispr-associated endoribonuclease cas6/csy4 (20 kDa, Protein from Selenomonas sp.)
- Hnh endonuclease (39 kDa, Protein from Selenomonas sp.)
- Type i-f crispr-associated protein csy3 (37 kDa, Protein from Selenomonas sp.)
- Dna (5'-d(p*gp*tp*gp*cp*gp*gp*a)-3') (2 kDa, DNA from Selenomonas sp.)
- Dna (37-mer) (11 kDa, DNA from Selenomonas sp.)
Cryo-EM structure of Cas8-HNH system at partial R-loop state
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8z0l
Q-score: 0.549
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Hypothetical protein j6n51_11000 (28 kDa, Protein from Selenomonas sp.)
- Type i-f crispr-associated protein csy3 (37 kDa, Protein from Selenomonas sp.)
- Rna (69-mer) (22 kDa, RNA from Selenomonas sp.)
- Type i-f crispr-associated endoribonuclease cas6/csy4 (20 kDa, Protein from Selenomonas sp.)
- Cryo-em structure of cas8-hnh system at partial r-loop state (Complex from Selenomonas sp.)
- Hnh endonuclease (39 kDa, Protein from Selenomonas sp.)
- Dna (32-mer) (9 kDa, DNA from Selenomonas sp.)
- Dna (5'-d(p*gp*tp*gp*cp*gp*gp*a)-3') (2 kDa, DNA from Selenomonas sp.)
Cryo-EM structure of Cas8-HNH system at target free state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8zdy
Q-score: 0.42
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- A protein (38 kDa, Protein from Selenomonas sp.)
- A protein (28 kDa, Protein from Selenomonas sp.)
- A protein (39 kDa, Protein from Selenomonas sp.)
- Rna (58-mer) (22 kDa, RNA from Selenomonas sp.)
- A protein (20 kDa, Protein from Selenomonas sp.)
- A protein (Complex from Selenomonas sp.)
Cryo-EM structure of Cas8-HNH system at ssDNA-bound state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8znr
Q-score: 0.505
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Rna (56-mer) (22 kDa, RNA from Selenomonas sp.)
- Protein structure (39 kDa, Protein from Selenomonas sp.)
- Dna (35-mer) (10 kDa, DNA from Selenomonas sp.)
- Protein complex (Complex from Selenomonas sp.)
- Protein structure (28 kDa, Protein from Selenomonas sp.)
- Protein structure (20 kDa, Protein from Selenomonas sp.)
- Protein structure (37 kDa, Protein from Selenomonas sp.)
SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67
Qin Q, Jiang X, Huo L, Qian J, Yu H, Zhu H, Du W, Cao Y, Zhang X, Huang Q
J Nanobiotechnology (2024) 22 pp. 58-58 [ Pubmed: 38341574 DOI: doi:10.1186/s12951-024-02329-3 ]
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike protein in complex with a self-assembling trivalent nanobody tr67 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Trivalent nanobody (Complex from synthetic construct)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrg
Q-score: 0.227
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone (Complex from Homo sapiens)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Histone methyltransferase and nucleosome complex (Complex)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
- Histone,suv420h1 (Complex from Xenopus laevis)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrd
Q-score: 0.484
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- Histone methyltransferase and nucleosome complex (Complex from Homo sapiens)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
