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 ]
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
Borealin N-terminus in complex with H3.T3p-nucleosome
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 8ruq
Q-score: 0.618
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromosome passenger complex localisation module (borealin n-terminus only) (Complex from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from unidentified)
- Dna (147-mer) (46 kDa, DNA from unidentified)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
SIRT7-H3K36MTUnucleosome complex
Carlos MY, Babatunde E, Polina F, Esther S, Dongchun N, Henning S, Beat F
To Be Published
- [[(2~{r},3~{a}~{r},5~{r},6~{r},6~{a}~{r})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (673 Da, Ligand)
- Histone h2a type 2-a (13 kDa, Protein from Homo sapiens)
- Nad-dependent protein deacetylase sirtuin-7 (45 kDa, Protein from Homo sapiens)
- Dna (149-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (149-mer) (46 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- K36 structure (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
Haspin bound to nucleosome in position 2
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 9b2t
Q-score: 0.502
Hicks CW, Gliech CR, Zhang X, Rahman S, Vasquez S, Holland AJ, Wolberger C
To Be Published
- Haspin bound to nucleosome (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- Serine/threonine-protein kinase haspin (40 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
Empty Nucleosome with 601 widom sequence
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9e1y
Q-score: 0.685
Malik D, Deshmukh A, Bilokapic S, Halic M
bioRxiv (2025) [ Pubmed: 39803580 DOI: doi:10.1101/2024.12.31.630910 ]
- Empty nucleosome with 601 widom sequence (Complex from Xenopus laevis)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Cryo-EM structure of native H2AK119bu nucleosome at 2.6
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8vlr
Q-score: 0.602
Shen XY, Chen CX, Wang Y, Zheng W, Zheng JH, Jones AE, Zhu B, Zhang H, Lyons C, Rijal A, Moley JA, Cao GS, Liu K, Winn R, McGinty RK, Zhang K, Wang HB
To Be Published
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (136-mer) (41 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Native h2ak119bu nucleosome (Complex from Homo sapiens)
- Dna (136-mer) (42 kDa, DNA from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-a (10 kDa, Protein from Homo sapiens)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egx
Q-score: 0.25
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egy
Q-score: 0.256
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egz
Q-score: 0.261
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)