Structure of DDM1-nucleosome complex in the apo state
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8wh5
Q-score: 0.394
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (51 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (51 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in the apo state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in ADP state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8wh8
Q-score: 0.403
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in ADP-BeFx state
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8wh9
Q-score: 0.336
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Resolution: 4.05 Å
EM Method: Single-particle
Fitted PDBs: 8wha
Q-score: 0.306
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
Structure of nucleosome core particle of Arabidopsis thaliana
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8whb
Q-score: 0.5
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
Structure of nucleosome-bound SRCAP-C in the apo state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x15
Q-score: 0.218
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna (137-mer) (42 kDa, DNA from synthetic construct)
- Structure of nucleosome-bound srcap-c in the apo state (Complex from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Dna (137-mer) (41 kDa, DNA from synthetic construct)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1, n-terminally processed (41 kDa, Protein from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x19
Q-score: 0.292
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-befx-bound state (Complex from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the ADP-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x1c
Q-score: 0.297
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ Pubmed: 38331872 DOI: doi:10.1038/s41421-023-00640-1 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-bound state (Complex from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
The nucleosome-bound human PBAF complex
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7y8r
Q-score: 0.172
Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y
Nat Commun (2022) 13 pp. 7644-7644 [ Pubmed: 36496390 DOI: doi:10.1038/s41467-022-34859-5 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Unkown (1 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e member 1 (46 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Nucleosome-bound human pbaf complex (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Actb protein (fragment) (41 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Swi/snf complex subunit smarcc2 (133 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Homo sapiens)
- Protein polybromo-1 (184 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Bromodomain-containing protein 7 (74 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily b member 1 (44 kDa, Protein from Homo sapiens)
- Dna (213-mer) (65 kDa, DNA from Homo sapiens)
- Dna (213-mer) (65 kDa, DNA from Homo sapiens)
- Phd finger protein 10 (56 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Unknown (2 kDa, Protein from Homo sapiens)
- Unknown (8 kDa, Protein from Homo sapiens)
- Transcription activator brg1 (184 kDa, Protein from Homo sapiens)
- At-rich interactive domain-containing protein 2 (197 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily d member 1 (58 kDa, Protein from Homo sapiens)
- Unknown (1 kDa, Protein from Homo sapiens)
Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6j99
Q-score: 0.132
Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J
Cell Res (2019) 29 pp. 330-333 [ DOI: doi:10.1038/s41422-019-0146-7 Pubmed: 30770869 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (250 kDa, Complex from African clawed frog)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (Complex from Human)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (Complex)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Dna (144-mer) (45 kDa, DNA from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)