Capsid of DT57C bacteriophage in the full state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ho3
Q-score: 0.524
Ayala R, Moiseenko AV, Chen TH, Kulikov EE, Golomidova AK, Orekhov PS, Street MA, Sokolova OS, Letarov AV, Wolf M
Nat Commun (2023) 14 pp. 8205-8205 [ DOI: doi:10.1038/s41467-023-43824-9 Pubmed: 38081816 ]
- Escherichia phage dt57c (Virus from Escherichia phage DT57C)
- Major head protein (50 kDa, Protein from Escherichia phage DT57C)
Capsid of DT57C bacteriophage in the empty state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8hqk
Q-score: 0.507
Ayala R, Moiseenko AV, Chen TH, Kulikov EE, Golomidova AK, Orekhov PS, Street MA, Sokolova OS, Letarov AV, Wolf M
Nat Commun (2023) 14 pp. 8205-8205 [ DOI: doi:10.1038/s41467-023-43824-9 Pubmed: 38081816 ]
- Escherichia phage dt57c (Virus from Escherichia phage DT57C)
- Major head protein (50 kDa, Protein from Escherichia phage DT57C)
Neck of DT57C bacteriophage in the full state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8hqo
Q-score: 0.441
Ayala R, Moiseenko AV, Chen TH, Kulikov EE, Golomidova AK, Orekhov PS, Street MA, Sokolova OS, Letarov AV, Wolf M
Nat Commun (2023) 14 pp. 8205-8205 [ DOI: doi:10.1038/s41467-023-43824-9 Pubmed: 38081816 ]
- Tape measure protein (132 kDa, Protein from Escherichia phage DT57C)
- Tail terminator protein (18 kDa, Protein from Escherichia phage DT57C)
- Tequintavirus dt57c (Virus from Tequintavirus DT57C)
- Portal protein (45 kDa, Protein from Escherichia phage DT57C)
- Head completion protein (19 kDa, Protein from Escherichia phage DT57C)
Baseplate of DT57C bacteriophage in the full state
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8hqz
Q-score: 0.446
Ayala R, Moiseenko AV, Chen TH, Kulikov EE, Golomidova AK, Orekhov PS, Street MA, Sokolova OS, Letarov AV, Wolf M
Nat Commun (2023) 14 pp. 8205-8205 [ DOI: doi:10.1038/s41467-023-43824-9 Pubmed: 38081816 ]
- L-shaped tail fiber assembly (113 kDa, Protein from Escherichia phage DT57C)
- Tape measure protein (132 kDa, Protein from Escherichia phage DT57C)
- Minor tail protein (34 kDa, Protein from Escherichia phage DT57C)
- Baseplate hub protein (107 kDa, Protein from Escherichia phage DT57C)
- L-shaped tail fiber assembly (15 kDa, Protein from Escherichia phage DT57C)
- Tail tube protein (50 kDa, Protein from Escherichia phage DT57C)
- Escherichia phage dt57c (Virus from Escherichia phage DT57C)
- Distal tail protein (22 kDa, Protein from Escherichia phage DT57C)
Tail tube of DT57C bacteriophage in the full state
Resolution: 4.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 8hrg
Q-score: 0.347
Ayala R, Moiseenko AV, Chen TH, Kulikov EE, Golomidova AK, Orekhov PS, Street MA, Sokolova OS, Letarov AV, Wolf M
Nat Commun (2023) 14 pp. 8205-8205 [ DOI: doi:10.1038/s41467-023-43824-9 Pubmed: 38081816 ]
- Escherichia phage dt57c (Virus from Escherichia phage DT57C)
- Tail tube protein (50 kDa, Protein from Escherichia phage DT57C)
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
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ino80 complex subunit c (20 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Ino80 complex subunit b (38 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Chromatin-remodeling atpase ino80 (177 kDa, Protein from Homo sapiens)
- Complex of human ino80core bound to a wt nucleosome (1 MDa, Complex from Homo sapiens)
Structure of nucleotide-bound Tel1/ATM
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6s8f
Q-score: 0.315
Yates LA, Williams RM, Hailemariam S, Ayala R, Burgers P, Zhang X
Structure (2020) 28 pp. 96-104.e3 [ DOI: doi:10.1016/j.str.2019.10.012 Pubmed: 31740029 ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Serine/threonine-protein kinase tel1,serine/threonine-protein kinase tel1,serine/threonine-protein kinase tel1,serine/threonine-protein kinase tel1,serine/threonine-protein kinase tel1 (292 kDa, Protein from Saccharomyces cerevisiae)
- Tel1/atm (Complex from Saccharomyces cerevisiae)
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 [ Pubmed: 30309918 DOI: doi:10.1126/science.aat7716 ]
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Swr1-nucleosome complex (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Remodeller (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (14 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))
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (154-mer) (47 kDa, DNA from synthetic construct)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (154-mer) (47 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin remodeller-nucleosome complex at 4.5 A resolution.
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6gen
Q-score: 0.195
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 [ Pubmed: 30309918 DOI: doi:10.1126/science.aat7716 ]
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Swr1-nucleosome complex (1 MDa, Complex)
- Dna (173-mer) (53 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Remodeller (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (14 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))
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (173-mer) (53 kDa, DNA from synthetic construct)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histones (Complex 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 ]
- Human ino80 (Complex from synthetic construct)
- Ino80 complex subunit b (38 kDa, Protein from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone subunits (Complex from Homo sapiens)
- Dna (142-mer) (62 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (142-mer) (61 kDa, DNA from synthetic construct)
- Nucleosome (Complex from Homo sapiens)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Complex of core human ino80 with nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna helicase ino80 (146 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)