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 ]
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
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 ]
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from unidentified)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromosome passenger complex localisation module (borealin n-terminus only) (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Dna (147-mer) (46 kDa, DNA from unidentified)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
SIRT7-H3K36MTUnucleosome complex
Carlos MY, Babatunde E, Polina F, Esther S, Dongchun N, Henning S, Beat F
To Be Published
- K36 structure (Complex from Homo sapiens)
- Nad-dependent protein deacetylase sirtuin-7 (45 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- [[(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)
- Dna (149-mer) (45 kDa, DNA from Homo sapiens)
- Dna (149-mer) (46 kDa, DNA 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
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Haspin bound to nucleosome (Complex from Xenopus laevis)
- Serine/threonine-protein kinase haspin (40 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Empty nucleosome with 601 widom sequence (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
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
- Native h2ak119bu nucleosome (Complex from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Dna (136-mer) (41 kDa, DNA from Homo sapiens)
- Histone h2b type 1-a (10 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (136-mer) (42 kDa, DNA 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 [ Pubmed: 39666822 DOI: doi:10.1126/science.adn6319 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Setd2 downstream complex (Complex from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Parafibromin (60 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 rpabc5 (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 [ Pubmed: 39666822 DOI: doi:10.1126/science.adn6319 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Setd2 downstream complex (Complex from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Parafibromin (60 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 rpabc5 (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 [ Pubmed: 39666822 DOI: doi:10.1126/science.adn6319 ]
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Setd2 downstream complex (Complex from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Parafibromin (60 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 rpabc5 (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9b3i
Q-score: 0.293
Fung HYJ, Jiou J, Niesman AB, Bernardes NE, Chook YM
J Cell Biol (2025) 224 [ Pubmed: 39601790 DOI: doi:10.1083/jcb.202408193 ]
- Gtp-binding nuclear protein (21 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Complex of kap114 bound to ran gtpase gsp1, h2a-h2b and nap1 (Complex from Saccharomyces cerevisiae)
- Nap1 isoform 1 (48 kDa, Protein from Saccharomyces cerevisiae)
- Kap114 isoform 1 (114 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Histone h2a (13 kDa, Protein from Saccharomyces cerevisiae)