Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses
Matsui A, Spangler CJ, Elferich J, Shiozaki M, Jean N, Zhao X, Qin M, Zhong H, Yu Z, Gouaux E
To Be Published
Image sets:
KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7uv9
Q-score: 0.42
Spangler CJ, Skrajna A, Foley CA, Nguyen A, Budziszewski GR, Azzam DN, Arteaga EC, Simmons HC, Smith CB, Wesley NA, Wilkerson EM, McPherson JE, Kireev D, James LI, Frye SV, Goldfarb D, McGinty RK
Nat Chem Biol (2023) 19 pp. 624-632 [ Pubmed: 36797403 DOI: doi:10.1038/s41589-023-01256-y ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Lysine-specific demethylase 2a (79 kDa, Protein from Homo sapiens)
- Dna (185-mer) (56 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (185-mer) (57 kDa, DNA from synthetic construct)
- Kdm2a-nucleosome complex stabilized by h3k36c-unc8015 covalent conjugate (310 kDa, Complex from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Fe (iii) ion (55 Da, Ligand)
- N-heptanoyl-n-hydroxy-beta-alanine (217 Da, Ligand)
KDM2B-nucleosome complex stabilized by H3K36C-UNC8015 covalent conjugate
Spangler CJ, Skrajna A, Foley CA, Nguyen A, Budziszewski GR, Azzam DN, Arteaga EC, Simmons HC, Smith CB, Wesley NA, Wilkerson EM, McPherson JE, Kireev D, James LI, Frye SV, Goldfarb D, McGinty RK
Nat Chem Biol (2023) 19 pp. 624-632 [ Pubmed: 36797403 DOI: doi:10.1038/s41589-023-01256-y ]
- Human histone h3 (Protein from Homo sapiens)
- Human histone h4 (Protein from Homo sapiens)
- Kdm2b-nucleosome complex stabilized by h3k36c-unc8015 covalent conjugate (320 kDa, Complex from Homo sapiens)
- Dna 185-mer (DNA from synthetic construct)
- Human histone h2b (Protein from Homo sapiens)
- Lysine-specific demethylase 2b (kdm2b) (Protein from Homo sapiens)
- Human histone h2a (Protein from Homo sapiens)
Structure of VRK1 C-terminal tail bound to nucleosome core particle
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7tan
Q-score: 0.56
Budziszewski GR, Zhao Y, Spangler CJ, Kedziora KM, Williams MR, Azzam DN, Skrajna A, Koyama Y, Cesmat AP, Simmons HC, Arteaga EC, Strauss JD, Kireev D, McGinty RK
Nucleic Acids Res (2022) 50 pp. 4355-4371 [ Pubmed: 35390161 DOI: doi:10.1093/nar/gkac198 ]
- Serine/threonine-protein kinase vrk1 (45 kDa, Protein from Homo sapiens)
- Structure of vrk1 c-terminal tail bound to nucleosome core particle (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b type 1-c/e/f/g/i, serine/threonine-protein kinase vrk1 (Complex from Homo sapiens)
- Widom 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Widom 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
Uncrosslinked VRK1-nucleosome complex
Budziszewski GR, Zhao Y, Spangler CJ, Kedziora KM, Williams MR, Azzam DN, Skrajna A, Koyama Y, Cesmat AP, Simmons HC, Arteaga EC, Strauss JD, Kireev D, McGinty RK
Nucleic Acids Res (2022) 50 pp. 4355-4371 [ Pubmed: 35390161 DOI: doi:10.1093/nar/gkac198 ]
- Histone h3.2 (Protein from Homo sapiens)
- Structure of vrk1 c-terminal tail bound to nucleosome core particle (Complex)
- Widom 601 dna (185-mer) (DNA from synthetic construct)
- Vaccinia-related kinase 1 (Protein from Homo sapiens)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b type 1-c/e/f/g/i, serine/threonine-protein kinase vrk1 (Complex from Homo sapiens)
- Histone h2a (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2b (Protein from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7jo9
Q-score: 0.483
Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q
Science (2020) 370 pp. 450-454 [ DOI: doi:10.1126/science.abd0609 Pubmed: 32913000 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 1:1 cgas-nucleosome complex (250 kDa, Complex from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7joa
Q-score: 0.474
Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q
Science (2020) 370 pp. 450-454 [ DOI: doi:10.1126/science.abd0609 Pubmed: 32913000 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Mus musculus)
- 2:1 cgas-nucleosome complex (290 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q
Science (2020) 370 pp. 450-454 [ DOI: doi:10.1126/science.abd0609 Pubmed: 32913000 ]
- 1:1 cgas-nucleosome complex (250 kDa, Complex)