Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7oob
Q-score: 0.566
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Rna (3 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Complex between the transcribing rna polymerase ii and tcr factors in the presence of adp-bef3. (Complex)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna excision repair protein ercc-6 and ercc-8, dna damage-binding protein 1 (Complex from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opc
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to csb, crl4csa, uvssa, paf and spt6. (Complex)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7oo3
Q-score: 0.521
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna repair proteins, csb element and scaffold protein (Complex from Homo sapiens)
- Rna (3 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Csb element (2 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase ii elongation complex with csb, csa-ddb1 and uvssa. (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna directed rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Nts, ts & rna (Complex from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7oop
Q-score: 0.421
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Complex between transcribing pol ii, tcr factors and elongation factors spt6 and paf. (Complex)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (133 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Supplementory proteins (Complex from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7opd
Q-score: 0.472
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Pig)
- Cullin-4a (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Complex from Mus musculus)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Pig)
- Rna (14 kDa, RNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Pig)
- Zinc ion (65 Da, Ligand)
- Rpol4c domain-containing protein (16 kDa, Protein from Pig)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Pig)
- Rna polymerase ii subunit k (7 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Supplementary proteins (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Pig)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Mus musculus)
- Nts, rna, ts (Complex from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Transcribing pol ii bound to trc factors, spt6 and paf. (Complex)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Pig)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
Cryo-electron tomogram of FIB-milled U2OS cells
Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E
Nat Protoc (2020) 15 pp. 2041-2070 [ DOI: doi:10.1038/s41596-020-0320-x Pubmed: 32405053 ]
Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome
Resolution: 15.0 Å
EM Method: Single-particle
Fitted PDBs: 6tda
Q-score: 0.081
Wagner FR, Dienemann C, Wang H, Stutzer A, Tegunov D, Urlaub H, Cramer P
Nature (2020) 579 pp. 448-451 [ DOI: doi:10.1038/s41586-020-2088-0 Pubmed: 32188943 ]
- Chromatin remodelling complex rsc ('remodels the structure of chromatin') bound to a nucleosome (Complex)
- Rsc core (Complex from Saccharomyces cerevisiae S288C)
- Atpase domain of sth1 bound to the nucleosome (Complex from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-i (72 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Unknown protein (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-j (73 kDa, DNA from synthetic construct)
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (126 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (13 kDa, Protein from Xenopus laevis)