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 h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (51 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in the apo state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (sense strand) (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein 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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- 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-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a.6 (13 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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Histone h2a.6 (13 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 ]
- Structure of the nucleosome core particle of arabidopsis thaliana (200 kDa, Complex from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Dna (sense strand) (45 kDa, DNA from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8ol1
Q-score: 0.4
Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A
Nature (2024) 627 pp. 873-879 [ DOI: doi:10.1038/s41586-024-07112-w Pubmed: 38418882 ]
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-n (10 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-j (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-h (11 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Cgas-spsb3-elobc complex (Complex from Homo sapiens)
- Histone h2b type 1-h (10 kDa, Protein from Homo sapiens)
- Spry domain-containing socs box protein 3 (27 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
Structure of yeast replisome associated with FACT and histone hexamer, Composite map
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8xgc
Q-score: 0.407
Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y
Nature (2024) 627 pp. 890-897 [ DOI: doi:10.1038/s41586-024-07152-2 Pubmed: 38448592 ]
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b.2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae)
- Dna (39-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Mediator of replication checkpoint protein 1 (124 kDa, Protein from Saccharomyces cerevisiae)
- Endogenous replisomes (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit pob3 (63 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (29 kDa, Protein from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna (51-mer) (15 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit spt16 (118 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
Yeast Set2 bound to a nucleosome containing oncohistone mutations
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ea5
Q-score: 0.473
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J
Cell Discov (2021) 7 pp. 32-32 [ DOI: doi:10.1038/s41421-021-00261-6 Pubmed: 33972509 ]
- Histone h4 (8 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 601-dna (44 kDa, DNA from synthetic construct)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-36 specific (26 kDa, Protein from Saccharomyces cerevisiae)
- The set2-nucleosome(h3k36m)complex structure (Complex from Xenopus laevis)
- Histone h3 (11 kDa, Protein from Xenopus laevis)
- 601-dna (44 kDa, DNA from synthetic construct)
- S-adenosylmethionine (398 Da, Ligand)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
Human SETD2 bound to a nucleosome containing oncohistone mutations
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7ea8
Q-score: 0.509
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J
Cell Discov (2021) 7 pp. 32-32 [ DOI: doi:10.1038/s41421-021-00261-6 Pubmed: 33972509 ]
- Histone h2a type 1-d (11 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Zinc ion (65 Da, Ligand)
- 601-dna (37 kDa, DNA from synthetic construct)
- Histone (Complex)
- S-adenosylmethionine (398 Da, Ligand)
- Histone h3.3 (11 kDa, Protein from Homo sapiens)
- Human setd2-ncp(h3.3k36m)-sam complex structure (Complex from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- 601-dna (37 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase setd2 (28 kDa, Protein from Homo sapiens)
- Histone h4 (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (Complex from Homo sapiens)
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 6upk
Q-score: 0.203
Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K
Nature (2020) 577 pp. 426-431 [ Pubmed: 31775157 DOI: doi:10.1038/s41586-019-1820-0 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Fact complex subunit ssrp1 (73 kDa, Protein from Homo sapiens)
- Fact_subnucleosome_complex_class1 (320 kDa, Complex from Homo sapiens)
- Fact complex subunit spt16 (109 kDa, Protein from Homo sapiens)
- Dna (79-mer) (24 kDa, DNA from Escherichia coli)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Dna (79-mer) (24 kDa, DNA from Escherichia coli)
- Histone h2a (14 kDa, Protein from Homo sapiens)