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- [ Pubmed: 39121853 DOI: doi:10.1016/j.molcel.2024.07.016 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- 186bp albn1 nucleosome in complex with scfv (Complex from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- Scfv (29 kDa, Protein from Mus musculus)
- Histone h3.1 (15 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- [ Pubmed: 39121853 DOI: doi:10.1016/j.molcel.2024.07.016 ]
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Foxa1 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Hepatocyte nuclear factor 3-alpha (50 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- [ Pubmed: 39121853 DOI: doi:10.1016/j.molcel.2024.07.016 ]
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Maltose/maltodextrin-binding periplasmic protein,transcription factor gata-4 (87 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Foxa1 and gata4 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8ybj
Q-score: 0.631
Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
Genes Cells (2024) 29 pp. 769-781 [ DOI: doi:10.1111/gtc.13143 Pubmed: 38972377 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- The human nucleosome containing h3.1 (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8ybk
Q-score: 0.598
Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
Genes Cells (2024) 29 pp. 769-781 [ DOI: doi:10.1111/gtc.13143 Pubmed: 38972377 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- The human nucleosome containing h3.1 e97k mutant (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j91
Q-score: 0.545
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ Pubmed: 38992002 DOI: doi:10.1038/s41467-024-49465-w ]
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Hta13 (14 kDa, Protein from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana histones (200 kDa, Complex from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j92
Q-score: 0.53
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
Nat Commun (2024) 15 pp. 5187-5187 [ Pubmed: 38992002 DOI: doi:10.1038/s41467-024-49465-w ]
- Dna (Complex)
- Dna (169-mer) (52 kDa, DNA from synthetic construct)
- Hta6 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome containing arabidopsis thaliana h2a.w (200 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Dna (169-mer) (51 kDa, DNA from synthetic construct)
- Htb9 (16 kDa, Protein from Arabidopsis thaliana)
- Nucleosome (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8xbw
Q-score: 0.219
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*ap*cp*cp*gp*cp*tp*tp*ap*ap*ap*cp*gp*cp*ap*cp*gp*tp*a)-3') (47 kDa, DNA from synthetic construct)
- Dna (5'-d(p*tp*ap*cp*gp*tp*gp*cp*gp*tp*tp*tp*ap*ap*gp*cp*gp*gp*t)-3') (47 kDa, DNA from synthetic construct)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
CX3CR1 nucleosome and wild type PU.1 complex
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8evh
Q-score: 0.509
Lian T, Guan R, Zhou BR, Bai Y
Nat Struct Mol Biol (2024) 31 pp. 633-643 [ DOI: doi:10.1038/s41594-023-01189-z Pubmed: 38267599 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcription factor pu.1 (32 kDa, Protein from Mus musculus)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- Single-chain variable fragment (29 kDa, Protein from Escherichia coli)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Nucleosome pu.1 complex (Complex from Homo sapiens)
- Histone h2a type 2-c (14 kDa, Protein from Homo sapiens)
- Dna (162-mer) (49 kDa, DNA from Mus musculus)
- Dna (162-mer) (50 kDa, DNA from Mus musculus)
CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8evi
Q-score: 0.559
Lian T, Guan R, Zhou BR, Bai Y
Nat Struct Mol Biol (2024) 31 pp. 633-643 [ DOI: doi:10.1038/s41594-023-01189-z Pubmed: 38267599 ]
- Dna (167-mer) (51 kDa, DNA from Mus musculus)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcription factor pu.1 (32 kDa, Protein from Mus musculus)
- Histone h2a type 2-c (14 kDa, Protein from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- Single-chain variable fragment (29 kDa, Protein from Escherichia coli)
- Nucleosome pu.1 mutant complex (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (14 kDa, Protein from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from Mus musculus)