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)
RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8s51
Q-score: 0.415
Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P
Mol Cell (2024) 84 pp. 1699-1710.e6 [ DOI: doi:10.1016/j.molcel.2024.03.016 Pubmed: 38604172 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib, iie and iif (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Template dna (42 kDa, DNA from unidentified adenovirus)
- Non-template dna (43 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa)
- Dna and rna (Complex from unidentified adenovirus)
- Transcription initiation factor iie subunit beta (33 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)
- Rna (2 kDa, RNA from unidentified adenovirus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Tata-box-binding protein, transcription initiation factor iia (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 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)
- Core initially transcribing complex with an ordered rna of 8 nt (Complex)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s52
Q-score: 0.431
Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P
Mol Cell (2024) 84 pp. 1699-1710.e6 [ DOI: doi:10.1016/j.molcel.2024.03.016 Pubmed: 38604172 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Template dna (42 kDa, DNA from unidentified adenovirus)
- Non-template dna (43 kDa, DNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa)
- Dna and rna (Complex from unidentified adenovirus)
- Transcription initiation factor iie subunit beta (33 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 rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Tata-box-binding protein, transcription initiation factor iib, iie and iif (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from unidentified adenovirus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Core initially transcribing complex with an ordered rna of 10 nt (Complex)
- Transcription initiation factor iia (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8s54
Q-score: 0.368
Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P
Mol Cell (2024) 84 pp. 1699-1710.e6 [ DOI: doi:10.1016/j.molcel.2024.03.016 Pubmed: 38604172 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (42 kDa, DNA from unidentified adenovirus)
- Non-template dna (43 kDa, DNA from unidentified adenovirus)
- Rna (4 kDa, RNA from unidentified adenovirus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa)
- Dna and rna (Complex from unidentified adenovirus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription factor iie subunit 1 and transcription factor iif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii early elongation complex bound to tfiie and tfiif - state b (Complex)
- 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)
- 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8s55
Q-score: 0.365
Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P
Mol Cell (2024) 84 pp. 1699-1710.e6 [ DOI: doi:10.1016/j.molcel.2024.03.016 Pubmed: 38604172 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Rna polymerase ii early elongation complex bound to tfiie and tfiif - state a (Complex)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Template dna (42 kDa, DNA from unidentified adenovirus)
- Non-template dna (43 kDa, DNA from unidentified adenovirus)
- Rna (4 kDa, RNA from unidentified adenovirus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa)
- Dna and rna (Complex from unidentified adenovirus)
- Transcription initiation factor iie subunit beta (33 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 rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- 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)
- Transcription factor iie and iif (Cell from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8s5n
Q-score: 0.386
Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P
Mol Cell (2024) 84 pp. 1699-1710.e6 [ DOI: doi:10.1016/j.molcel.2024.03.016 Pubmed: 38604172 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Template dna (42 kDa, DNA from unidentified adenovirus)
- Non-template dna (43 kDa, DNA from unidentified adenovirus)
- Rna (3 kDa, RNA from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa)
- Transcription initiation factor iie subunit beta (33 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 rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- 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)
- Core initially transcribing complex with and ordered rna of 12 nt (Complex from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Cryo-EM structure of the Nup98(298-327) fibril
Resolution: 2.67 Å
EM Method: Helical reconstruction
Fitted PDBs: 8ci8
Q-score: 0.609
Ibanez de Opakua A, Pantoja CF, Cima-Omori MS, Dienemann C, Zweckstetter M
Nat Commun (2024) 15 pp. 3797-3797 [ Pubmed: 38714656 DOI: doi:10.1038/s41467-024-48194-4 ]
- Nuclear pore complex protein nup98 (3 kDa, Protein from Homo sapiens)
- Nup98(298-327) (Complex from Homo sapiens)