Structure of an STK19-containing TC-NER complex
Resolution: 1.9 Å
EM Method: Single-particle
Fitted PDBs: 9bz0
Q-score: 0.448
Mevissen TET, Kummecke M, Schmid EW, Farnung L, Walter JC
Cell (2024) 187 pp. 7091-7106.e24 [ DOI: doi:10.1016/j.cell.2024.10.020 Pubmed: 39547228 ]
- Dna (49-mer) (27 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (35-mer) (27 kDa, DNA from synthetic construct)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Transcription-coupled nucleotide excision repair complex (Complex from Homo sapiens)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
ICP1 Csy-dsDNA complex (partial duplex)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8k27
Q-score: 0.46
To Be Published
- Csy4 (18 kDa, Protein from Vibrio phage ICP1 2004 A)
- Csy3 (33 kDa, Protein from Vibrio phage ICP1 2004 A)
- Csy1 (20 kDa, Protein from Vibrio phage ICP1 2004 A)
- Dna (25-mer) (7 kDa, DNA from Vibrio phage ICP1 2004 A)
- Dna (49-mer) (15 kDa, DNA from Vibrio phage ICP1 2004 A)
- Csy2 (27 kDa, Protein from Vibrio phage ICP1 2004 A)
- Csy complex (Complex from Vibrio phage ICP1 2004 A)
- Rna (60-mer) (19 kDa, RNA from Vibrio phage ICP1 2004 A)
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8ree
Q-score: 0.136
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
PNAS (2024) 121 pp. e2309670120-e2309670120 [ Pubmed: 38170755 DOI: doi:10.1073/pnas.2309670120 ]
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma-54 factor (36 kDa, Protein from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta' (152 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Rna polymerase-sigma54 initial transcribing complex - 9nt complex (Complex from Escherichia coli K-12)
- Rna (5'-r(p*gp*cp*cp*gp*cp*gp*ap*up*c)-3') (2 kDa, RNA from Klebsiella oxytoca)
- Dna (45-mer) (13 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (49-mer) (15 kDa, DNA from Klebsiella oxytoca)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex bent CRISPR repeat conformation
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8fyd
Q-score: 0.338
Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA
Nature (2023) 618 pp. 855-861 [ Pubmed: 37316664 DOI: doi:10.1038/s41586-023-06178-2 ]
- Dna (64-mer) (19 kDa, DNA from Megasphaera)
- Cas1:cas2-deddh:half-site integration complex (272 kDa, Complex from Megasphaera)
- Dna (13-mer) (13 kDa, DNA from Megasphaera)
- Dna (49-mer) (23 kDa, DNA from Megasphaera)
- Cas1 (35 kDa, Protein from Megasphaera)
- Cas2-deddh (32 kDa, Protein from Megasphaera)
- Dna (30-mer) (10 kDa, DNA from Megasphaera)
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 7w1y
Q-score: 0.595
Li J, Dong J, Wang W, Yu D, Fan X, Hui YC, Lee CSK, Lam WH, Alary N, Yang Y, Zhang Y, Zhao Q, Chen CL, Tye BK, Dang S, Zhai Y
Cell (2023) 186 pp. 98-111.e21 [ Pubmed: 36608662 DOI: doi:10.1016/j.cell.2022.12.008 ]
- Dna replication licensing factor mcm5 (82 kDa, Protein from Homo sapiens)
- Dna (49-mer) (14 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Isoform 2 of dna replication licensing factor mcm3 (96 kDa, Protein from Homo sapiens)
- Dna replication licensing factor mcm6 (93 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication licensing factor mcm4 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Human mini-chromosome maintenance complex (1 MDa, Complex from Homo sapiens)
- Dna replication licensing factor mcm7 (81 kDa, Protein from Homo sapiens)
- Dna (49-mer) (15 kDa, DNA from Homo sapiens)
- Dna replication licensing factor mcm2 (102 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Dna replication licensing factor mcm 2/3/4/5/6/7 (Complex from Homo sapiens)
Structure of the OgeuIscB-omega RNA-target DNA complex
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7xht
Q-score: 0.619
Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H
Nat Commun (2022) 13 pp. 6719-6719 [ Pubmed: 36344504 DOI: doi:10.1038/s41467-022-34378-3 ]
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Ogeuiscb (56 kDa, Protein from metagenome)
- Magnesium ion (24 Da, Ligand)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Iscb-omegarna (Complex from metagenome)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Dna (Complex)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Dna (49-mer) (15 kDa, DNA from synthetic construct)
Structure of RecT protein from Listeria innoccua phage A118 in complex with 83-mer annealed duplex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ub2
Q-score: 0.508
Caldwell BJ, Norris AS, Karbowski CF, Wiegand AM, Wysocki VH, Bell CE
Nat Commun (2022) 13 pp. 7855-7855 [ DOI: doi:10.1038/s41467-022-35572-z Pubmed: 36543802 ]
- Dna (49-mer) (15 kDa, DNA from Escherichia virus M13)
- Dna (49-mer) (14 kDa, DNA from Escherichia virus M13)
- Rect protein from listeria innocua phage a118, complexed with two complementary strands of ssdna that were added to the protein sequentially (602 kDa, Complex from Listeria innocua Clip11262)
- Rect (30 kDa, Protein from Listeria innocua Clip11262)
Cryo-EM structure of spyCas9-sgRNA-DNA dimer
Resolution: 5.26 Å
EM Method: Single-particle
Fitted PDBs: 7v59
Q-score: 0.153
Yang M, Sun R, Deng P, Yang Y, Wang W, Liu JG, Chen C
Chem Sci (2021) 12 pp. 12776-12784 [ DOI: doi:10.1039/d1sc02633j Pubmed: 34703564 ]
- Dna (49-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Ternary complex of spycas9 with sgrna and dna (Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
Cryo-EM structure of Rifamycin bound to E. coli RNAP and rrnBP1 promoter complex
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7szj
Q-score: 0.489
Rajeswaran W, Ashkar SR, Lee PH, Yeomans L, Shin Y, Franzblau SG, Murakami KS, Showalter HD, Garcia GA
Acs Infect Dis. (2022) 8 pp. 1422-1438 [ Pubmed: 35772744 DOI: doi:10.1021/acsinfecdis.1c00636 ]
- Rifampicin (822 Da, Ligand)
- Rifamycin bound to e. coli rnap and rrnbp1 promoter complex (Complex from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna (49-mer) (19 kDa, DNA from Escherichia coli K-12)
- Dna (57-mer) (19 kDa, DNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
Cre recombinase mutant (D33A/A36V/R192A) in complex with loxA DNA hairpin
Resolution: 3.91 Å
EM Method: Single-particle
Fitted PDBs: 7rhy
Q-score: 0.401
Stachowski K, Norris AS, Potter D, Wysocki VH, Foster MP
Nucleic Acids Res (2022) 50 pp. 1753-1769 [ Pubmed: 35104890 DOI: doi:10.1093/nar/gkac032 ]
- Dna (49-mer) (15 kDa, DNA from Escherichia phage P1)
- Recombinase cre (38 kDa, Protein from Escherichia phage P1)
- Complex of cre recombinase mutant d33a/a36v/r192a and loxa dna hairpin (54 kDa, Complex from Escherichia phage P1)