Resolution: 5.14 Å
EM Method: Single-particle
Fitted PDBs: 9dwu
Q-score: 0.122
Fisher RJ, Park K, Lee K, Pinjusic K, Vanasse A, Ennis CS, Ficcaro S, Marto J, Stransky S, Duke-Cohan J, Geethadevi A, Raabe E, Sidoli S, Hicks CW, Keskin DB, Wu CJ, Cole PA, Alani RM
bioRxiv (2024) [ Pubmed: 39713349 DOI: doi:10.1101/2024.12.12.627852 ]
- Lysine-specific histone demethylase 1a (74 kDa, Protein from Homo sapiens)
- Splicing factor u2af2 bound to the corest complex made up of lsd1 and rcor1 (Complex from Homo sapiens)
- Splicing factor u2af 65 kda subunit (8 kDa, Protein from Homo sapiens)
- Rest corepressor 1 (7 kDa, Protein from Homo sapiens)
Cryo-EM structure of a SIN3/HDAC complex from budding yeast
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8hpo
Q-score: 0.492
Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C
Nat Struct Mol Biol (2023) [ DOI: doi:10.1038/s41594-023-00975-z Pubmed: 37081318 ]
- Transcriptional regulatory protein dep1 (47 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein ume1 (51 kDa, Protein from Baker's yeast)
- The rpd3l complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein pho23 (37 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein sds3 (37 kDa, Protein from Baker's yeast)
- Phosphothreonine (199 Da, Ligand)
- Transcriptional regulatory protein sap30 (23 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Baker's yeast)
- Histone deacetylase rpd3 (48 kDa, Protein from Baker's yeast)
- Potassium ion (39 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulatory protein rxt3 (33 kDa, Protein from Baker's yeast)
- Histone deacetylase rpd3 (49 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein rxt2 (48 kDa, Protein from Baker's yeast)
Human menin in complex with H3K79Me2 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8gpn
Q-score: 0.459
Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD
Science (2023) 379 pp. 717-723 [ Pubmed: 36795828 DOI: doi:10.1126/science.adc9318 ]
- Isoform 2 of menin (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Isoform 2 of menin (67 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (Complex from Homo sapiens)
- Human menin in complex with nh3k79 dimethylated nucleosome (300 kDa, Complex from Xenopus laevis)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nh3k79 dimethylated nucleosome (Complex)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
antibody and nucleosome complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7k78
Q-score: 0.556
Guan R, Lian T, Zhou BR, He E, Wu C, Singleton M, Bai Y
Nat Commun (2021) 12 pp. 1763-1763 [ DOI: doi:10.1038/s41467-021-21985-9 Pubmed: 33741944 ]
- Cse4 (15 kDa, Protein from Saccharomyces cerevisiae)
- Dna (136-mer) (41 kDa, DNA from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Scfv (29 kDa, Protein from Mus musculus)
- Dna (136-mer) (42 kDa, DNA from Saccharomyces cerevisiae)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Scfv and nucleosome complex (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7k7g
Q-score: 0.3
Guan R, Lian T, Zhou BR, He E, Wu C, Singleton M, Bai Y
Nat Commun (2021) 12 pp. 1763-1763 [ DOI: doi:10.1038/s41467-021-21985-9 Pubmed: 33741944 ]
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (147-mer) (45 kDa, DNA from Saccharomyces cerevisiae)
- The nucleosome and gal4 domain complex (Complex from Saccharomyces cerevisiae)
- Dna (147-mer) (45 kDa, DNA from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Centromere dna-binding protein complex cbf3 subunit b (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
cryo-EM structure of human H2A.Z.2.2 nucleosome
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6m4d
Q-score: 0.311
Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z
EMBO J (2021) 40 pp. e105907-e105907 [ Pubmed: 33073403 DOI: doi:10.15252/embj.2020105907 ]
- H2a.z.2.2 nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (125-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- Dna (125-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a.v (12 kDa, Protein from Homo sapiens)
The ClassC RSC-Nucleosome Complex
Resolution: 10.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw5
Q-score: 0.062
Ye YP, Wu H, Chen KJ, Verma N, Cairns B, Gao N, Chen ZC
To Be Published
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of nucleosome-bound human BAF complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6ltj
Q-score: 0.007
He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B, Xu Y
Science (2020) 367 pp. 875-881 [ DOI: doi:10.1126/science.aaz9761 Pubmed: 32001526 ]
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily b member 1 (38 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e member 1 (46 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Xenopus laevis)
- Actin-like protein 6a (45 kDa, Protein from Homo sapiens)
- Dna (119-mer) (36 kDa, DNA from Homo sapiens)
- Swi/snf complex subunit smarcc2 (133 kDa, Protein from Homo sapiens)
- Zinc finger protein ubi-d4 (32 kDa, Protein from Homo sapiens)
- At-rich interactive domain-containing protein 1a (142 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound human baf complex (Complex)
- Dna (119-mer) (36 kDa, DNA from Homo sapiens)
- Nucleosome (Complex from Xenopus calcaratus)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Baf (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Transcription activator brg1 (184 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)
The ClassA RSC-Nucleosome Complex
Resolution: 7.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw3
Q-score: 0.086
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
The ClassB RSC-Nucleosome Complex
Resolution: 7.55 Å
EM Method: Single-particle
Fitted PDBs: 6kw4
Q-score: 0.099
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Saccharomyces cerevisiae S288C)
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))