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Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8j3r
Q-score: 0.174
Hino T, Omura NS, Nakagawa R, Togashi T, Takeda NS, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro H, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Siksnys V, Ohmori T, Hoshino A, Nureki O
To Be Published
- Rna (118-mer) (38 kDa, RNA from Sulfoacidibacillus thermotolerans)
- Dna (Complex from Sulfoacidibacillus thermotolerans)
- Ascas12f-hkra (Complex from Sulfoacidibacillus thermotolerans)
- Ascas12f-hkra-sgrnas3-5v7-target dna (Complex from Sulfoacidibacillus thermotolerans)
- Dna (38-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
- Transposase is605 orfb c-terminal domain-containing protein (49 kDa, Protein from Sulfoacidibacillus thermotolerans)
- Magnesium ion (24 Da, Ligand)
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
- Dna (37-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 8c5s
Q-score: 0.453
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K
Nature (2023) 622 pp. 872-879 [ Pubmed: 37821701 DOI: doi:10.1038/s41586-023-06643-y ]
- Mitochondrial transcription factor 1 (Complex from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (Complex from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpupapapapu) (1 kDa, RNA from Saccharomyces cerevisiae S288C)
- Non-template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (Complex from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase, mitochondrial (143 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpupapapapu) (Complex from Saccharomyces cerevisiae S288C)
- Yeast mitochondrial rna polymerase transcription initiation complex with 7-mer rna, pppgpgpupapapapu (ic7) (204 kDa, Complex)
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8c5u
Q-score: 0.446
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K
Nature (2023) 622 pp. 872-879 [ Pubmed: 37821701 DOI: doi:10.1038/s41586-023-06643-y ]
- Non-template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpupapapapupg) (2 kDa, RNA from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpupapapapupg) (Complex from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (Complex from Saccharomyces cerevisiae S288C)
- Yeast mitochondrial rna polymerase transcription initiation complex with 8-mer rna, pppgpgpupapapapupg (ic8) (204 kDa, Complex)
- Dna (37-mer) (Complex from Saccharomyces cerevisiae S288C)
- Template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (Complex from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase, mitochondrial (143 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8q63
Q-score: 0.398
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K
Nature (2023) 622 pp. 872-879 [ Pubmed: 37821701 DOI: doi:10.1038/s41586-023-06643-y ]
- Rna (pppgpgpupapapapupg) (2 kDa, RNA from Saccharomyces cerevisiae S288C)
- Rna (pppgpgpupapapapupg) (Complex from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (Complex from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (Complex from Saccharomyces cerevisiae S288C)
- Alternate state of yeast mitochondrial rna polymerase transcription initiation complex with 8-mer rna, pppgpgpupapapapupg, and a wider polymerase cleft (ic8') (204 kDa, Complex from Saccharomyces cerevisiae S288C)
- Template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (Complex from Saccharomyces cerevisiae S288C)
- Mitochondrial transcription factor 1 (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase, mitochondrial (143 kDa, Protein from Saccharomyces cerevisiae S288C)
- Non-template dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8syi
Q-score: 0.491
Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS
PNAS (2024) 121 pp. e2311480121-e2311480121 [ Pubmed: 38354263 DOI: doi:10.1073/pnas.2311480121 ]
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
- Rna (5'-r(p*up*up*cp*ap*ap*ap*gp*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Magnesium ion (24 Da, Ligand)
- Cyrnap-elongation complex (Complex from Synechococcus elongatus)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Zinc ion (65 Da, Ligand)
Thermus thermophilus RNA polymerase elongation complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8hsg
Q-score: 0.434
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Rna (5'-r(p*cp*cp*ap*cp*ap*up*cp*cp*ap*cp*cp*u)-3') (39 kDa, RNA from synthetic construct)
- Rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Dna (27-mer) (54 kDa, DNA from synthetic construct)
- Dna (37-mer) (57 kDa, DNA from DNA molecule)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
Mediator-PIC Early (Tail A + Upstream DNA Activator)
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 7uik
Q-score: 0.091
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574- [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
- Mediator of rna polymerase ii transcription subunit 2 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 16 (111 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 5 (128 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Dna (38-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Regulatory protein gal4 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Med-picearly (taila+activator & dna class 1) (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 14 (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 15 (120 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
Mediator-PIC Early (Composite Model)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7uio
Q-score: 0.239
Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K
Mol Cell (2023) 83 pp. 574- [ DOI: doi:10.1016/j.molcel.2023.01.011 Pubmed: 36731470 ]
- Mediator of rna polymerase ii transcription subunit 2 (47 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 14 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae S288C)
- Aspartic acid (133 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Regulatory protein gal4 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Alanine (89 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (37-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- Threonine (119 Da, Ligand)
- Transcription elongation factor s-ii (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 16 (111 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb1 (162 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb1 (2 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 15 (120 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 5 (128 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (38-mer) (11 kDa, DNA from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae S288C)
- Med-picearly (Complex from Saccharomyces cerevisiae S288C)
CryoEM Structure of an Group II Intron Retroelement
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7uin
Q-score: 0.467
Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM
Science (2022) 378 pp. 627-634 [ Pubmed: 36356138 DOI: doi:10.1126/science.abq2844 ]
- Water (18 Da, Ligand)
- Ternary complex of rna, protein and dna (260 kDa, Complex from [Eubacterium] rectale)
- E.r iic intron (206 kDa, RNA from [Eubacterium] rectale)
- Magnesium ion (24 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Dna (37-mer) (11 kDa, DNA from [Eubacterium] rectale)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7z1z
Q-score: 0.19
Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P
Nat Commun (2022) 13 pp. 2416- [ DOI: doi:10.1038/s41467-022-29928-8 ]
- Dna (5'-d(*gp*cp*tp*gp*cp*gp*ap*gp*ap*tp*cp*cp*gp*cp*tp*cp*cp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)
- Dna (37-mer) (15 kDa, DNA from DNA molecule)
- Pol polyprotein (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Pc4 and sfrs1-interacting protein (11 kDa, Protein from Homo sapiens)
- Mvv stc intasome in complex with ledgf (480 kDa, Complex from Visna/maedi virus EV1 KV1772)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(p*tp*tp*gp*ap*tp*tp*ap*gp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)