Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9gd0
Q-score: 0.528
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (250-mer) (76 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (250-mer) (77 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. (Complex from Xenopus laevis)
Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9gd1
Q-score: 0.332
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Dna (261-mer) (81 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp.
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 9gd2
Q-score: 0.295
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (248-mer) (77 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. (Complex from Xenopus laevis)
- Dna (248-mer) (76 kDa, DNA from synthetic construct)
Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9gd3
Q-score: 0.465
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Structural insights into human co-transcriptional capping - structure 1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4a
Q-score: 0.344
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (29-mer) (8 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*ap*ap*ap*cp*cp*cp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from unidentified)
Structural insights into human co-transcriptional capping - structure 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8p4b
Q-score: 0.434
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (35-mer) (10 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*gp*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (7 kDa, RNA from unidentified)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Dna (5'-d(p*ap*gp*cp*gp*gp*cp*gp*gp*ap*gp*cp*cp*ap*gp*cp*ap*gp*gp*gp*ap*gp*cp*tp*g)-3') (7 kDa, DNA from unidentified)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 3
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8p4c
Q-score: 0.297
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from unidentified)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 4
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4d
Q-score: 0.348
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 5
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8p4e
Q-score: 0.297
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464- [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Rna (5'-d(*(mgt))-r(p*gp*ap*cp*ap*up*ap*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna (26-mer) (8 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna (35-mer) (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 6
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8p4f
Q-score: 0.29
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464- [ Pubmed: 37369200 DOI: doi:10.1016/j.molcel.2023.06.002 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- S-adenosylmethionine (398 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- 7n-methyl-8-hydroguanosine-5'-triphosphate (539 Da, Ligand)
- Rna (29-mer) (9 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)