CryoEM structure of Enterococcus italicus Csm-crRNA complex bound to AMPNPP
Jungfer K, Moravcik S, Garcia-Doval C, Knorlein A, Hall J, Jinek M
Nucleic Acids Res (2025) 53 [ Pubmed: 39817514 DOI: doi:10.1093/nar/gkae1277 ]
- Crispr system cms protein csm2 (16 kDa, Protein from Enterococcus italicus DSM 15952)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Enterococcus italicus DSM 15952)
- Crispr system cms protein csm4 (34 kDa, Protein from Enterococcus italicus DSM 15952)
- Crispr system cms protein csm5 (43 kDa, Protein from Enterococcus italicus DSM 15952)
- Csm-crrna complex bound to ampnpp with (csm1)1(csm2)2(csm3)3(csm4)1(csm5)1 stoichiometry (260 kDa, Complex from Enterococcus italicus DSM 15952)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (506 Da, Ligand)
- Rna (28-mer) (14 kDa, RNA from Enterococcus italicus DSM 15952)
- Magnesium ion (24 Da, Ligand)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (88 kDa, Protein from Enterococcus italicus DSM 15952)
WT CRISPR-Cas12a with a 8bp R-loop
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8sfi
Q-score: 0.36
Strohkendl I, Saha A, Moy C, Nguyen AH, Ahsan M, Russell R, Palermo G, Taylor DW
Mol Cell (2024) 84 pp. 2717-2731.e6 [ DOI: doi:10.1016/j.molcel.2024.06.007 Pubmed: 38955179 ]
- Dna (5'-d(p*cp*tp*tp*ap*tp*cp*ap*cp*tp*ap*ap*ap*ap*gp*ap*tp*cp*gp*gp*ap*ap*g)-3') (17 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
- Dna (5'-d(p*cp*tp*tp*cp*cp*gp*ap*tp*cp*tp*tp*tp*tp*ap*gp*tp*gp*ap*tp*a)-3') (17 kDa, DNA from synthetic construct)
- Rna (28-mer) (15 kDa, RNA from synthetic construct)
- Wt ascas12a incubated with 8bp-complementary target dna (Complex from Acidaminococcus sp. BV3L6)
Structure of Cas12a2 ternary complex
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8d4a
Q-score: 0.588
Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW
Nature (2023) 613 pp. 582-587 [ DOI: doi:10.1038/s41586-022-05560-w Pubmed: 36599980 ]
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (3 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Cas12a2 ternary complex (Complex from Sulfuricurvum sp. PC08-66)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from synthetic construct)
- Orfb_zn_ribbon domain-containing protein (143 kDa, Protein from Sulfuricurvum sp. PC08-66)
- Rna (28-mer) (8 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (41-mer) (13 kDa, RNA from synthetic construct)
- Water (18 Da, Ligand)
Structure of Cas12a2 ternary complex
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8d4b
Q-score: 0.517
Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW
Nature (2023) 613 pp. 582-587 [ DOI: doi:10.1038/s41586-022-05560-w Pubmed: 36599980 ]
- Orfb_zn_ribbon domain-containing protein (143 kDa, Protein from Sulfuricurvum sp. PC08-66)
- Rna (28-mer) (8 kDa, RNA from synthetic construct)
- Rna (41-mer) (13 kDa, RNA from synthetic construct)
- Cas12a2 ternary complex (Complex from Sulfuricurvum sp. PC08-66)
Transition state structure of Cpf1(Cas12a)I1 conformation
Resolution: 3.91 Å
EM Method: Single-particle
Fitted PDBs: 6gtc
Q-score: 0.386
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G
Cell (2018) 175 pp. 1856-1871.e21 [ DOI: doi:10.1016/j.cell.2018.10.045 Pubmed: 30503205 ]
- Transition state complex i1 conformation (180 kDa, Complex)
- Dna (Complex from Francisella tularensis subsp. novicida U112)
- Rna (28-mer) (Complex from Francisella tularensis subsp. novicida U112)
- Crispr-associated endonuclease cas12a (155 kDa, Protein from Francisella tularensis subsp. novicida U112)
- Dna (5'-d(p*cp*gp*ap*gp*cp*tp*cp*gp*tp*tp*ap*gp*ap*gp*ap*ap*g)-3') (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Crispr-associated endonuclease cas12a (Complex from Francisella tularensis subsp. novicida U112)
- Dna (5'-d(p*tp*gp*ap*cp*tp*tp*cp*tp*cp*tp*ap*ap*cp*ap*ap*gp*cp*tp*cp*g)-3') (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Rna (28-mer) (13 kDa, RNA from Francisella tularensis subsp. novicida U112)
Transient state structure of CRISPR-Cpf1 (Cas12a). I2 conformation
Resolution: 4.24 Å
EM Method: Single-particle
Fitted PDBs: 6gtd
Q-score: 0.384
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G
Cell (2018) 175 pp. 1856-1871.e21 [ DOI: doi:10.1016/j.cell.2018.10.045 Pubmed: 30503205 ]
- Crispr-associated endonuclease cas12a (155 kDa, Protein from Francisella tularensis subsp. novicida (strain U112))
- Dna (5'-d(p*cp*gp*ap*gp*cp*tp*cp*gp*tp*tp*ap*gp*ap*gp*ap*ap*gp*t)-3') (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Crispr-associated endonuclease cas12a (Complex from Francisella tularensis subsp. novicida U112)
- Transition state complex i2 conformation (180 kDa, Complex)
- Dna (5'-d(p*tp*gp*ap*cp*tp*tp*cp*tp*cp*tp*ap*ap*cp*ap*ap*gp*cp*tp*cp*g)-3') (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Rna (28-mer) (13 kDa, RNA from Francisella tularensis subsp. novicida U112)
- Nucleic acids (Complex from Francisella tularensis subsp. novicida U112)
Transition state structure of Cpf1(Cas12a)I4 conformation
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 6gtg
Q-score: 0.466
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G
Cell (2018) 175 pp. 1856-1871.e21 [ DOI: doi:10.1016/j.cell.2018.10.045 Pubmed: 30503205 ]
- Dna (32-mer) (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Dna (Complex from Francisella tularensis subsp. novicida U112)
- Rna (28-mer) (Complex from Francisella tularensis subsp. novicida U112)
- Crispr-associated endonuclease cas12a (155 kDa, Protein from Francisella tularensis subsp. novicida U112)
- Dna (5'-d(p*cp*gp*ap*gp*cp*tp*cp*gp*tp*tp*ap*gp*ap*gp*ap*ap*gp*t)-3') (16 kDa, DNA from Francisella tularensis subsp. novicida U112)
- Crispr-associated endonuclease cas12a (Complex from Francisella tularensis subsp. novicida U112)
- Transition state complex i4 conformation (180 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Rna (40-mer) (13 kDa, RNA from Francisella tularensis subsp. novicida U112)
- Water (18 Da, Ligand)