Cryo-EM structure of nucleosome containing Widom603 DNA
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8rgm
Q-score: 0.352
Motorin NA, Afonin D, Armeev GA, Moiseenko A, Zhao L, Vasiliev V, Oleinikov P, Shaytan A, Shi X, Studitsky V, Sokolova O
To Be Published
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Widom 603 dna sequence (44 kDa, DNA from synthetic construct)
- Widom 603 dna sequence (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Human nucleosome containing widom 603 dna sequence (Complex from Homo sapiens)
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex 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)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8vfx
Q-score: 0.559
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- 186bp albn1 nucleosome in complex with scfv (Complex from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- Scfv (29 kDa, Protein from Mus musculus)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8vfy
Q-score: 0.463
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Foxa1 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8vfz
Q-score: 0.27
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Foxa1 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8vg0
Q-score: 0.482
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,transcription factor gata-4 (87 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (159-mer) (57 kDa, DNA from synthetic construct)
- Dna (159-mer) (57 kDa, DNA from synthetic construct)
- Gata4 in complex with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome
Resolution: 2.48 Å
EM Method: Single-particle
Fitted PDBs: 8vg1
Q-score: 0.541
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,transcription factor gata-4 (87 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Foxa1 and gata4 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Human canonical 601 DNA nucleosome
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8jbx
Q-score: 0.43
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ DOI: doi:10.1093/nar/gkae825 Pubmed: 39329259 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone and 601 dna (Complex)
- 601 dna (Complex)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (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)
Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 8jcc
Q-score: 0.398
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ DOI: doi:10.1093/nar/gkae825 Pubmed: 39329259 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- H2bfwt nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Human H2BFWTH100R nucleosome with 601 DNA
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8jcd
Q-score: 0.445
Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T
Nucleic Acids Res (2024) 52 pp. 11612-11625 [ DOI: doi:10.1093/nar/gkae825 Pubmed: 39329259 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone and 601 dna (Complex)
- 601 dna (Complex)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)