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 ]
- Dna (Complex from synthetic construct)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Chromobox protein homolog 5 (22 kDa, Protein from Homo sapiens)
- Hp1alpha dimer bound to h2a.z nucleosome (288 kDa, Complex from Escherichia coli)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna widom601 (208bp) strand2 (63 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 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 [ DOI: doi:10.1038/s41422-024-01009-z Pubmed: 39103524 ]
- Dna (651 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.1 (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b (Complex from Xenopus laevis)
- 12x177bp-h5 chromatin (Complex)
- Histone h5 (21 kDa, Protein from Gallus gallus)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Linker histone h5 (Complex from Gallus gallus)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (660 kDa, DNA from synthetic construct)
- Widom 601 dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein 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 h3.3 (15 kDa, Protein from Homo sapiens)
- Dna (128-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 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)
- Dna (128-mer) (51 kDa, DNA from synthetic construct)
Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b0a
Q-score: 0.483
Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S
Nat Commun (2024) 15 pp. 1000-1000 [ Pubmed: 38307862 DOI: doi:10.1038/s41467-024-45237-8 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Complex between alc1 and a site-specifically parylated nucleosome (304 kDa, Complex from Homo sapiens)
H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8peo
Q-score: 0.548
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- H3k36me2 nucleosome-ledgf/p75 pwwp domain complex (Complex from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8pep
Q-score: 0.399
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- H3k36me2 nucleosome-ledgf/p75 pwwp domain complex - pose 2 (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- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iif (Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iib (Complex from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iia (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)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Unassigned peptide, likely xpb (698 Da, 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 rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
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- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- General transcription factor iih (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iie subunit 1 (22 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iif (Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Nucleosome (protein) (Complex from Xenopus laevis)
- General transcription factor iib (Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iia (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)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iie (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
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- [ Pubmed: 37148879 DOI: doi:10.1016/j.molcel.2023.04.011 ]
- Nucleosome (dna) (Complex from unidentified adenovirus)
- General transcription factor iia (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Non-template dna (64 kDa, DNA from unidentified adenovirus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Mammalian rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- General transcription factor iib (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- General transcription factor iif (Complex from Homo sapiens)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii core pre-initiation complex with the proximal +1 nucleosome (1 MDa, Complex)
- Zinc ion (65 Da, Ligand)
- Template dna (64 kDa, DNA from unidentified adenovirus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)