Cryo-EM structure of the Cas9d-sgRNA-target DNA complex
To Be Published
- A protein (Complex from metagenome)
- Dna (5'-d(p*cp*gp*gp*gp*tp*cp*ap*ap*ap*tp*g)-3') (11 kDa, DNA from metagenome)
- Rna (144-mer) (51 kDa, RNA from metagenome)
- Zinc ion (65 Da, Ligand)
- Dna (32-mer) (11 kDa, DNA from metagenome)
- A protein (86 kDa, Protein from metagenome)
Cryo-EM structure of the Cas9d-sgRNA complex
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8zq9
Q-score: 0.47
To Be Published
- Rna (128-mer) (51 kDa, RNA from metagenome)
- A protein (86 kDa, Protein from metagenome)
- A protein (Complex from metagenome)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1038/s44318-024-00229-8 Pubmed: 39251884 ]
- Cryo-em structure of cas8-hnh system at full r-loop state (Complex 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.)
- Hnh endonuclease (39 kDa, Protein from Selenomonas sp.)
- Dna (5'-d(p*gp*tp*gp*cp*gp*gp*a)-3') (2 kDa, DNA from Selenomonas sp.)
- Hypothetical protein j6n51_11000 (28 kDa, Protein 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 [ DOI: doi:10.1038/s44318-024-00229-8 Pubmed: 39251884 ]
- Type i-f crispr-associated protein csy3 (37 kDa, Protein from Selenomonas sp.)
- Rna (69-mer) (22 kDa, RNA from Selenomonas sp.)
- Dna (32-mer) (9 kDa, DNA 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.)
- Cryo-em structure of cas8-hnh system at partial r-loop state (Complex from Selenomonas sp.)
- Hypothetical protein j6n51_11000 (28 kDa, Protein 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 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 [ DOI: doi:10.1038/s44318-024-00229-8 Pubmed: 39251884 ]
- Dna (35-mer) (10 kDa, DNA from Selenomonas sp.)
- Protein structure (20 kDa, Protein from Selenomonas sp.)
- Rna (56-mer) (22 kDa, RNA from Selenomonas sp.)
- Protein complex (Complex from Selenomonas sp.)
- Protein structure (28 kDa, Protein from Selenomonas sp.)
- Protein structure (37 kDa, Protein from Selenomonas sp.)
- Protein structure (39 kDa, Protein from Selenomonas sp.)
Cryo-EM structure of CTR-bound type VII CRISPR-Cas complex at post-state I
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8yhd
Q-score: 0.5
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ DOI: doi:10.1038/s41586-024-07815-0 Pubmed: 39143216 ]
- Rna (53-mer) (21 kDa, RNA from metagenome)
- A protein (70 kDa, Protein from metagenome)
- Zinc ion (65 Da, Ligand)
- Rna (35-mer) (16 kDa, RNA from metagenome)
- A protein (22 kDa, Protein from metagenome)
- A protein (Complex from metagenome)
- A protein (27 kDa, Protein from metagenome)
Cryo-EM structure of CTR-bound type VII CRISPR-Cas complex at substrate-engaged state II
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8z4j
Q-score: 0.507
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ DOI: doi:10.1038/s41586-024-07815-0 Pubmed: 39143216 ]
- Rna (38-mer) (19 kDa, RNA from metagenome)
- Zinc ion (65 Da, Ligand)
- Protein structure (70 kDa, Protein from metagenome)
- Protein structure (22 kDa, Protein from metagenome)
- A protein (Complex from metagenome)
- Protein structure (27 kDa, Protein from metagenome)
- Rna (34-mer) (19 kDa, RNA from metagenome)
Cryo-EM structure of CTR-bound type VII CRISPR-Cas complex at substrate-engaged state I
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8z4l
Q-score: 0.531
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ DOI: doi:10.1038/s41586-024-07815-0 Pubmed: 39143216 ]
- A protein (Complex from metagenome)
- Rna (40-mer) (19 kDa, RNA from metagenome)
- A protein (27 kDa, Protein from metagenome)
- A protein (70 kDa, Protein from metagenome)
- A protein (22 kDa, Protein from metagenome)
- Rna (49-mer) (19 kDa, RNA from metagenome)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8kde
Q-score: 0.548
Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z
Nat Commun (2024) 15 pp. 5211-5211 [ Pubmed: 38890314 DOI: doi:10.1038/s41467-024-49532-2 ]
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- Cryo-em structure of an intermediate-state complex during the process of photosystem ii repair (Complex from Chlamydomonas reinhardtii)
- Uncharacterized protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 1 (prf1) (13 kDa, Protein from Chlamydomonas reinhardtii)
- Thylakoid enriched factor 14 (tef14) (20 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 2 (prf2) (12 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Pheophytin a (871 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
Overall cryo-EM map of an intermediate-state complex during the process of photosystem II repair