Structure of a native Drosophila melanogaster octameric nucleosome
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 9mu4
Q-score: 0.442
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Dna (164-mer) (50 kDa, DNA from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Natively purified octameric nucleosome from drosophila melanogaster (240 MDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna (164-mer) (50 kDa, DNA from Drosophila melanogaster)
Structure of a native Drosophila melanogaster hexameric nucleosome
Resolution: 6.3 Å
EM Method: Single-particle
Fitted PDBs: 9mu5
Q-score: 0.206
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Histone h3 (10 kDa, Protein from Drosophila melanogaster)
- Natively purified hexameric nucleosome from drosophila melanogaster (220 MDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna (133-mer) (41 kDa, DNA from Drosophila melanogaster)
- Dna (133-mer) (40 kDa, DNA from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 9mu9
Q-score: 0.202
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb9 (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Drosophila melanogaster)
- Non-template dna (50 kDa, DNA from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Drosophila melanogaster)
- Rna (3 kDa, RNA from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
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 ]
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- H3.t3p-nucleosome (Complex 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)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Borealin (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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 (15 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)
- Chromosome passenger complex localisation module (borealin n-terminus only) (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Dna (147-mer) (47 kDa, DNA from unidentified)
- Dna (147-mer) (46 kDa, DNA from unidentified)
- 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)
Nucleosome containing a 1-nt gap at SHL-4.5
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9dwf
Q-score: 0.526
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- Nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwg
Q-score: 0.364
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwh
Q-score: 0.384
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwi
Q-score: 0.405
Ryan BJ, Weaver TM, Freudenthal BD
To Be Published
- 601 i strand (damaged strand 1) (35 kDa, DNA from synthetic construct)
- 601 k strand (damaged strand 2) (8 kDa, DNA from synthetic construct)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-4.5 (Complex from Homo sapiens)
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9dwk
Q-score: 0.297
Weaver TM, Ryan BJ, Freudenthal BD
To Be Published
- Dna polymerase beta (38 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Dna polymerase beta bound to a nucleosome containing a 1-nt gap at shl-3.5 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 601 i strand (damaged strand 1) (32 kDa, DNA from synthetic construct)
- 601 k strand (damaged strand 2) (12 kDa, DNA from synthetic construct)
- 601 j strand (non-damaged strand) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)