Arabidopsis thaliana R2T complex
Palacios-Abella A, Lopez-Perrote A, Fonseca S, Urbez C, Rubio V, Boskovic J, Llorca O, Alabadi D
To Be Published
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 1 (53 kDa, Protein from Arabidopsis thaliana)
- Ruvb-like helicase (54 kDa, Protein from Arabidopsis thaliana)
- At1g56440 (59 kDa, Protein from Arabidopsis thaliana)
- Atr2t complex (700 kDa, Complex from Arabidopsis thaliana)
Cryo-EM structure of native SWR1 bound to DNA (composite structure)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9b1d
Q-score: 0.435
Louder RK, Park G, Ye Z, Cha JS, Gardner AM, Lei Q, Ranjan A, Hollmuller E, Stengel F, Pugh BF, Wu C
Cell (2024) 187 pp. 6849-6864.e18 [ DOI: doi:10.1016/j.cell.2024.09.007 Pubmed: 39357520 ]
- Helicase swr1 (178 kDa, Protein from Saccharomyces cerevisiae W303)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae W303)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Native swr1 bound to dna. (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Native swr1 complex (Complex from Saccharomyces cerevisiae)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Ruvb-like protein 1 (91 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9b1e
Q-score: 0.191
Louder RK, Park G, Ye Z, Cha JS, Gardner AM, Lei Q, Ranjan A, Hollmuller E, Stengel F, Pugh BF, Wu C
Cell (2024) 187 pp. 6849-6864.e18 [ Pubmed: 39357520 DOI: doi:10.1016/j.cell.2024.09.007 ]
- Zinc ion (65 Da, Ligand)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae W303)
- Native swr1 bound to nucleosome. (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna (214-mer) (65 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Native swr1 complex (Complex from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Helicase swr1 (178 kDa, Protein from Saccharomyces cerevisiae W303)
- Ruvb-like protein 1 (91 kDa, Protein from Saccharomyces cerevisiae W303)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae W303)
- Histone h3 (15 kDa, Protein from Drosophila melanogaster)
- Dna (214-mer) (66 kDa, DNA from synthetic construct)
- Swr1-complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae W303)
SWR1-nucleosome complex in configuration 1
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qku
Q-score: 0.363
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ Pubmed: 39506114 DOI: doi:10.1038/s41586-024-08152-y ]
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
SWR1-nucleosome complex in configuration 2
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 8qkv
Q-score: 0.185
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ Pubmed: 39506114 DOI: doi:10.1038/s41586-024-08152-y ]
- Magnesium ion (24 Da, Ligand)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Dna (194-mer) (60 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (194-mer) (59 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qyv
Q-score: 0.324
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ DOI: doi:10.1016/j.molcel.2024.08.015 Pubmed: 39226902 ]
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome complex (Complex from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qz0
Q-score: 0.293
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ DOI: doi:10.1016/j.molcel.2024.08.015 Pubmed: 39226902 ]
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h2a.z-specific chaperone chz1 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome-dimer complex (Complex from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.z (14 kDa, Protein from Saccharomyces cerevisiae S288C)
SWR1 lacking Swc5 subunit in complex with hexasome
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9fbw
Q-score: 0.193
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ DOI: doi:10.1016/j.molcel.2024.08.015 Pubmed: 39226902 ]
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna (112-mer) (34 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swr1 lacking swc5 subunit in complex with hexasome (Complex from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (112-mer) (34 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
CryoEM Structure INO80core Hexasome complex composite map state1
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oo7
Q-score: 0.556
Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S
Science (2023) 381 pp. 313-319 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)
INO80 core bound to hexasome composite map of state 2
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8oop
Q-score: 0.554
Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S
Science (2023) 381 pp. 313-319 [ DOI: doi:10.1126/science.adf6287 Pubmed: 37384673 ]
- Ruvb-like protein 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Dna strand 2 (70 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Ruvb-like protein 1 (50 kDa, Protein from Thermochaetoides thermophila)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna strand 1 (69 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Chromatin-remodeling atpase ino80 (130 kDa, Protein from Thermochaetoides thermophila)
- Chromatin remodeler ino80 (Complex from Thermochaetoides thermophila)
- Actin-related protein 5 (87 kDa, Protein from Thermochaetoides thermophila)
- Chromatin-remodeling complex subunit ies6 (23 kDa, Protein from Thermochaetoides thermophila)
- Ino80 core module in complex with hexasome (861 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ino eighty subunit 2 (53 kDa, Protein from Thermochaetoides thermophila)
- Histones (Complex from Homo sapiens)