Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eoz
Q-score: 0.465
Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C
Nat Commun (2024) 15 pp. 9407-9407 [ DOI: doi:10.1038/s41467-024-53811-3 Pubmed: 39477986 ]
- Widom 601 dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Widom 601 dna (145-mer) (45 kDa, DNA from synthetic construct)
- Nucleosome core particle (Complex from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (Complex from synthetic construct)
- Binary complex of human 8-oxoguanine glycosylase with nucleosome core particle (Complex)
- N-glycosylase/dna lyase (40 kDa, Protein from Homo sapiens)
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 ]
- Dna (214-mer) (66 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 1 (91 kDa, Protein from Saccharomyces cerevisiae W303)
- Histone h2a (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna (214-mer) (65 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Native swr1 bound to nucleosome. (1 MDa, Complex from Saccharomyces cerevisiae)
- Helicase swr1 (178 kDa, Protein from Saccharomyces cerevisiae W303)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae W303)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swr1-complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae W303)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae W303)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Histone h3 (15 kDa, Protein from Drosophila melanogaster)
- Native swr1 complex (Complex from Saccharomyces cerevisiae)
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
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)
Native SUV420H1 bound to 167-bp nucleosome
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8jhg
Q-score: 0.456
Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W
Cell Discov (2023) 9 pp. 120-120 [ DOI: doi:10.1038/s41421-023-00620-5 Pubmed: 38052811 ]
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Histone-lysine n-methyltransferase kmt5b (41 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- S-adenosylmethionine (398 Da, Ligand)
- Cryo-em structure of the native suv420h1 bound to 167-bp nucleosome (246 kDa, Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
Native SUV420H1 bound to 167-bp nucleosome
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8jhf
Q-score: 0.433
Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W
Cell Discov (2023) 9 pp. 120-120 [ DOI: doi:10.1038/s41421-023-00620-5 Pubmed: 38052811 ]
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Histone-lysine n-methyltransferase kmt5b (41 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- S-adenosylmethionine (398 Da, Ligand)
- Cryo-em structure of the native suv420h1 bound to 167-bp nucleosome (246 kDa, Complex from Homo sapiens)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
Structure of Bre1-nucleosome complex - state3
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8t3t
Q-score: 0.535
Nat Struct Mol Biol (2023) 30 pp. 1623-1627 [ DOI: doi:10.1038/s41594-023-01137-x Pubmed: 37872231 ]
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase bre1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Bre1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Xenopus laevis)