Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
Resolution: 7.5 Å
EM Method: Single-particle
Fitted PDBs: 9eoq
Q-score: 0.105
Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H
Nano Letters (2024) 24 pp. 5031-5038 [ Pubmed: 38602296 DOI: doi:10.1021/acs.nanolett.4c00915 ]
Cryo-EM structure of Rous sarcoma virus strand transfer complex
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8e14
Q-score: 0.366
Bera S, Shi K, Aihara H, Grandgenett DP, Pandey KK
J Biol Chem (2023) 299 pp. 104730-104730 [ DOI: doi:10.1016/j.jbc.2023.104730 Pubmed: 37084813 ]
- Dna (5'-d(*ap*ap*tp*gp*tp*tp*gp*tp*cp*tp*tp*ap*tp*gp*cp*ap*ap*tp*ap*cp*tp*c)-3') (6 kDa, DNA from Rous sarcoma virus - Prague C)
- Integrase (30 kDa, Protein from Rous sarcoma virus - Prague C)
- Dna (42-mer) (13 kDa, DNA from Rous sarcoma virus - Prague C)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(*ap*gp*tp*gp*tp*cp*tp*tp*cp*tp*tp*cp*tp*tp*tp*c)-3') (4 kDa, DNA from Rous sarcoma virus - Prague C)
- Rsv strand transfer complex (257 kDa, Complex from Rous sarcoma virus - Prague C)
Cryo-EM structure of precleavage Cre tetrameric complex
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 7rhx
Q-score: 0.526
Stachowski K, Norris AS, Potter D, Wysocki VH, Foster MP
Nucleic Acids Res (2022) 50 pp. 1753-1769 [ DOI: doi:10.1093/nar/gkac032 Pubmed: 35104890 ]
- Precleavage synaptic complex of cre recombinase mutant k201a and loxp dna (54 kDa, Complex from Escherichia phage P1)
- Dna (42-mer) (13 kDa, DNA from Escherichia phage P1)
- Recombinase cre (38 kDa, Protein from Escherichia phage P1)
- Dna (42-mer) (12 kDa, DNA from Escherichia phage P1)
Structure of a 9 base pair RecA-D loop complex.
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7jy9
Q-score: 0.476
Yang H, Zhou C, Dhar A, Pavletich NP
Nature (2020) 586 pp. 801-806 [ DOI: doi:10.1038/s41586-020-2820-9 Pubmed: 33057191 ]
- Dna (42-mer) (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Escherichia coli)
- Reca-d loop complex (Complex from Escherichia coli)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Protein reca (35 kDa, Protein from Escherichia coli)
- Dna (42-mer) (13 kDa, DNA from Escherichia coli)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6j4z
Q-score: 0.244
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Rna (5'-r(p*gp*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Spt5 (101 kDa, Protein from Komagataella pastoris)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex bound with spt4/5 and foreign dna, stalled at shl(-1) of the nucleosome (Complex from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 6a5l
Q-score: 0.182
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (Complex from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))