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)
CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA.
Ali-Ahmad A, Mors M, Carrer M, Li X, Bilokapic S, Halic M, Cascella M, Sekulic N
bioRxiv (2025) [ DOI: doi:10.1101/2024.12.31.630874 Pubmed: 39803555 ]
- 2x(cenp-a/h4)2 di-tetrasome assembled on alpha-satellite dna. (200 MDa, Complex from Homo sapiens)
- Histone h3-like centromeric protein a (15 kDa, Protein from Homo sapiens)
- 147 bp human alpha-satellite dna (45 kDa, DNA from Homo sapiens)
- 147 bp alpha-satellite dna (45 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Snf2h bound nucleosome complex - ClassC1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9e1u
Q-score: 0.595
Malik D, Deshmukh A, Bilokapic S, Halic M
bioRxiv (2025) [ Pubmed: 39803580 DOI: doi:10.1101/2024.12.31.630910 ]
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (152-mer) (46 kDa, DNA from Homo sapiens)
- Snf2h bound nucleosome complex-classc1 (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Snf2h bound nucleosome complex - ClassD1
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9e1x
Q-score: 0.499
Malik D, Deshmukh A, Bilokapic S, Halic M
bioRxiv (2025) [ Pubmed: 39803580 DOI: doi:10.1101/2024.12.31.630910 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (150-mer) (46 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Snf2h bound nucleosome complex-classd1 (Complex from Homo sapiens)
- Dna (149-mer) (46 kDa, DNA from Homo sapiens)
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)
Resolution: 5.14 Å
EM Method: Single-particle
Fitted PDBs: 9dwu
Q-score: 0.122
Fisher RJ, Park K, Lee K, Pinjusic K, Vanasse A, Ennis CS, Ficcaro S, Marto J, Stransky S, Duke-Cohan J, Geethadevi A, Raabe E, Sidoli S, Hicks CW, Keskin DB, Wu CJ, Cole PA, Alani RM
bioRxiv (2024) [ Pubmed: 39713349 DOI: doi:10.1101/2024.12.12.627852 ]
- Lysine-specific histone demethylase 1a (74 kDa, Protein from Homo sapiens)
- Splicing factor u2af2 bound to the corest complex made up of lsd1 and rcor1 (Complex from Homo sapiens)
- Splicing factor u2af 65 kda subunit (8 kDa, Protein from Homo sapiens)
- Rest corepressor 1 (7 kDa, Protein from Homo sapiens)
Cryo-EM structure of Nap1 core
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9b23
Q-score: 0.311
Fung HYJ, Jiou J, Niesman AB, Bernardes NE, Chook YM
J Cell Biol (2025) 224 [ Pubmed: 39601790 DOI: doi:10.1083/jcb.202408193 ]
- Nap1 isoform 1 (36 kDa, Protein from Saccharomyces cerevisiae)
- Complex of kap114 bound to nap1 and histone h2a-h2b (72 kDa, Complex from Saccharomyces cerevisiae)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7i
Q-score: 0.443
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8x7j
Q-score: 0.391
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)