Structural basis for the linker histone H5-nucleosome binding and chromatin compaction
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8xjv
Q-score: 0.424
Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P
Cell Res (2024) 34 pp. 707-724 [ Pubmed: 39103524 DOI: doi:10.1038/s41422-024-01009-z ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.1 (Complex from Xenopus laevis)
- Histone h5 (21 kDa, Protein from Gallus gallus)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Widom 601 dna (Complex from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (660 kDa, DNA from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- 12x177bp-h5 chromatin (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (651 kDa, DNA from synthetic construct)
- Histone h2b (Complex from Xenopus laevis)
- Linker histone h5 (Complex from Gallus gallus)
- Histone h2a (Complex from Xenopus laevis)
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iie (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- General transcription factor iib (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8byq
Q-score: 0.187
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iia (Complex from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iih (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iie (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
- General transcription factor iib (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8bz1
Q-score: 0.244
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Rna polymerase ii core pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- General transcription factor iia (Complex from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Mammalian rna polymerase ii (Complex 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 rpb3 (31 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- General transcription factor iib (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7kbd
Q-score: 0.489
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nucleosome in interphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7kbe
Q-score: 0.445
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Xenopus laevis)
- Nucleosome isolated from metaphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6zhx
Q-score: 0.625
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Crosslinked complex of alc1 regulatory linker and the nucleosome (206 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Water (18 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6zhy
Q-score: 0.516
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- A hexasome (nucleosome lacking one of the two h2a-h2b dimers) with its acidic patch bound by the alc1 linker regulatory region. (170 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2
Resolution: 4.36 Å
EM Method: Single-particle
Fitted PDBs: 6r1u
Q-score: 0.198
Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A
Cell Rep (2019) 27 pp. 387-399.e7 [ DOI: doi:10.1016/j.celrep.2019.03.061 Pubmed: 30970244 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Lysine-specific histone demethylase 1b (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Putative oxidoreductase glyr1 (13 kDa, Protein from Homo sapiens)
- Putative oxidoreductase glyr1 (Complex from Homo sapiens)
- Histone (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Lsd2/npac(214-225)/nucleosome (290 kDa, Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Lysine-specific histone demethylase 1b (87 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6nog
Q-score: 0.356
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Poised state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- H2b-ub nucleosome (Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Dot1l (Complex from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone core (Complex from Xenopus laevis)