Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8rup
Q-score: 0.551
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome
Resolution: 6.3 Å
EM Method: Single-particle
Fitted PDBs: 8uxq
Q-score: 0.143
To Be Published
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Hp1alpha dimer bound to h2a.z nucleosome (288 kDa, Complex from Escherichia coli)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromobox protein homolog 5 (22 kDa, Protein from Homo sapiens)
- Dna widom601 (208bp) strand2 (63 kDa, DNA from synthetic construct)
- Dna widom601 (208bp) strand1 (64 kDa, DNA from synthetic construct)
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)
The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9b3p
Q-score: 0.455
Jung H, Sokolova V, Lee G, Stevens VR, Tan D
Epigenomes (2024) 8 [ DOI: doi:10.3390/epigenomes8020021 Pubmed: 38920622 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (128-mer) (45 kDa, DNA from synthetic construct)
- Dna (128-mer) (51 kDa, DNA from synthetic construct)
- Nucleosome containing histone variants h3.3 and h2a.z (288 kDa, Complex from Escherichia coli)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
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)
Human menin in complex with H3K79Me2 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8gpn
Q-score: 0.459
Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD
Science (2023) 379 pp. 717-723 [ DOI: doi:10.1126/science.adc9318 Pubmed: 36795828 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Nh3k79 dimethylated nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Isoform 2 of menin (67 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (Complex from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Human menin in complex with nh3k79 dimethylated nucleosome (300 kDa, Complex from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Isoform 2 of menin (Complex)
Active state Dot1 bound to the H4K16ac nucleosome, Ubiquitin focused map
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Active state dot1 bound to the h4k16 acetylated nucleosome (Complex from Saccharomyces cerevisiae)
- Polyubiquitin-b (Protein from Xenopus laevis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Dna (146-mer) (Complex from Synthetic)
- Polyubiquitin-b (Complex from Homo sap)
Active state Dot1 bound to the unacetylated H4 nucleosome, Ubiquitin focused map
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Polyubiquitin-b (Protein from Xenopus laevis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Dna (146-mer) (Complex from Synthetic)
- Active state dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Polyubiquitin-b (Complex from Homo sap)