Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7zi4
Q-score: 0.462
Vance NR, Ayala R, Willhoft O, Tvardovskiy A, McCormack EA, Bartke T, Zhang X, Wigley DB
To Be Published
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Chromatin-remodeling atpase ino80 (177 kDa, Protein from Homo sapiens)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Ino80 complex subunit c (20 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Complex of human ino80core bound to a wt nucleosome (1 MDa, Complex from Homo sapiens)
- Ino80 complex subunit b (38 kDa, Protein from Homo sapiens)
RecBCD-DNA in complex with the phage protein Abc2
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8b1t
Q-score: 0.463
Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS
eLife (2022) 11 [ DOI: doi:10.7554/eLife.83409 Pubmed: 36533901 ]
- Dna (70-mer) (Complex from synthetic construct)
- Dna (70-mer) (21 kDa, DNA from synthetic construct)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli)
- Recbcd-abc2-dna complex (Complex)
- Recbcd enzyme subunit recd (66 kDa, Protein from Escherichia coli)
- Recbcd enzyme subunit recb, recc and recd (Complex from Escherichia coli)
- Recbcd enzyme subunit recb (134 kDa, Protein from Escherichia coli)
- Anti-recbcd protein 2 (11 kDa, Protein from Salmonella phage P22)
- Magnesium ion (24 Da, Ligand)
- Anti-recbcd protein 2 (Complex from Salmonella phage P22)
RecBCD-DNA in complex with the phage protein Abc2 and host PpiB
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8b1u
Q-score: 0.387
Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS
eLife (2022) 11 [ DOI: doi:10.7554/eLife.83409 Pubmed: 36533901 ]
- Recbcd enzyme subunits recb, recc and recd (Complex from Escherichia coli)
- Dna (70-mer) (Complex from synthetic construct)
- Dna (70-mer) (21 kDa, DNA from synthetic construct)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli)
- Recbcd enzyme subunit recd (66 kDa, Protein from Escherichia coli)
- Recbcd-abc2-ppib-dna complex (Complex)
- Recbcd enzyme subunit recb (134 kDa, Protein from Escherichia coli)
- Anti-recbcd protein 2 (11 kDa, Protein from Salmonella phage P22)
- Magnesium ion (24 Da, Ligand)
- Anti-recbcd protein 2 (Complex from Salmonella phage P22)
Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6qxf
Q-score: 0.309
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB
Mol Cell (2019) 75 pp. 90-101.e5 [ Pubmed: 31080012 DOI: doi:10.1016/j.molcel.2019.04.020 ]
- Crispr-associated protein csn2 (25 kDa, Protein from Streptococcus thermophilus)
- Dna (Complex from Escherichia coli BL21(DE3))
- Crispr-associated endoribonuclease cas2 (13 kDa, Protein from Streptococcus thermophilus)
- Crispr-associated endonuclease cas1 (35 kDa, Protein from Streptococcus thermophilus)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli BL21(DE3))
- Cas1-cas2-csn2 (Complex from Streptococcus thermophilus)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli BL21(DE3))
- Calcium ion (40 Da, Ligand)
- Cas1-cas2-csn2-dna monomer complex (530 kDa, Complex)
Cas1-Cas2-Csn2-DNA dimer complex from the Type II-A CRISPR-Cas system
Resolution: 8.9 Å
EM Method: Single-particle
Fitted PDBs: 6qxt
Q-score: 0.197
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB
Mol Cell (2019) 75 pp. 90-101.e5 [ Pubmed: 31080012 DOI: doi:10.1016/j.molcel.2019.04.020 ]
- Crispr-associated protein csn2 (25 kDa, Protein from Streptococcus thermophilus)
- Dna (Complex from Escherichia coli BL21(DE3))
- Crispr-associated endoribonuclease cas2 (13 kDa, Protein from Streptococcus thermophilus)
- Cas1-cas2-csn2-dna monomer complex (1 MDa, Complex)
- Dna (64-mer) (19 kDa, DNA from Escherichia coli BL21(DE3))
- Crispr-associated endonuclease cas1 (35 kDa, Protein from Streptococcus thermophilus)
- Cas1-cas2-csn2 (Complex from Streptococcus thermophilus)
- Calcium ion (40 Da, Ligand)
- Dna (64-mer) (20 kDa, DNA from Escherichia coli BL21(DE3))
Segment of the Cas1-Cas2-Csn2-DNA filament complex from the Type II-A CRISPR-Cas system
Resolution: 9.1 Å
EM Method: Single-particle
Fitted PDBs: 6qy3
Q-score: 0.163
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB
Mol Cell (2019) 75 pp. 90-101.e5 [ Pubmed: 31080012 DOI: doi:10.1016/j.molcel.2019.04.020 ]
- Crispr-associated protein csn2 (25 kDa, Protein from Streptococcus thermophilus)
- Dna (Complex from Escherichia coli BL21(DE3))
- Minimal unit of the cas1-cas2-csn2 (Complex from Streptococcus thermophilus)
- Crispr-associated endoribonuclease cas2 (13 kDa, Protein from Streptococcus thermophilus)
- Crispr-associated endonuclease cas1 (35 kDa, Protein from Streptococcus thermophilus)
- Dna (66-mer) (20 kDa, DNA from Escherichia coli BL21(DE3))
- Dna (66-mer) (20 kDa, DNA from Escherichia coli BL21(DE3))
- Calcium ion (40 Da, Ligand)
- Cas1-cas2-csn2-dna monomer complex (530 kDa, Complex)
Chromatin remodeller-nucleosome complex at 3.6 A resolution.
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6gej
Q-score: 0.372
Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M, Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS, Wigley DB
Science (2018) 362 [ DOI: doi:10.1126/science.aat7716 Pubmed: 30309918 ]
- Swr1-nucleosome complex (1 MDa, Complex)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (154-mer) (47 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Remodeller (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Histone (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Dna (154-mer) (47 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Vacuolar protein sorting-associated protein 72 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of the human INO80 complex bound to nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6hts
Q-score: 0.181
Ayala R, Willhoft O, Aramayo RJ, Wilkinson M, McCormack EA, Ocloo L, Wigley DB, Zhang X
Nature (2018) 556 pp. 391-395 [ DOI: doi:10.1038/s41586-018-0021-6 Pubmed: 29643506 ]
- Ino80 complex subunit b (38 kDa, Protein from synthetic construct)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Human ino80 (Complex from synthetic construct)
- Dna (142-mer) (62 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (142-mer) (61 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone subunits (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Complex of core human ino80 with nucleosome (Complex from Homo sapiens)
- Dna helicase ino80 (146 kDa, Protein from Homo sapiens)
High resolution INO80 core complex
Resolution: 4.06 Å
EM Method: Single-particle
Fitted PDBs: 5oaf
Q-score: 0.315
Aramayo RJ, Willhoft O, Ayala R, Bythell-Douglas R, Wigley DB, Zhang X
Nat Struct Mol Biol (2018) 25 pp. 37-44 [ Pubmed: 29323271 DOI: doi:10.1038/s41594-017-0003-7 ]
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Human ino80 core complex (800 kDa, Complex from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Cryo-EM structure of RecBCD+DNA complex revealing activated nuclease domain
Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 5ld2
Q-score: 0.401
Wilkinson M, Chaban Y, Wigley DB
eLife (2016) 5 [ Pubmed: 27644322 DOI: doi:10.7554/eLife.18227 ]
- Recbcd enzyme subunit recb,recbcd enzyme subunit recb,recbcd enzyme subunit recb (133 kDa, Protein from Escherichia coli (strain K12))
- Fork-hairpin dna (70-mer) (21 kDa, DNA from Endothia gyrosa)
- Ternary complex of recbcd with forked dna substrate and adpnp (350 kDa, Complex from Escherichia coli K12)
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Recbcd enzyme subunit recd (67 kDa, Protein from Escherichia coli (strain K12))
- Recbcd enzyme subunit recc (128 kDa, Protein from Escherichia coli (strain K12))