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MYC-MAX bound to a nucleosome at SHL+5.8
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ott
Q-score: 0.411
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH
Nature (2023) 619 pp. 385-393 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Pentanedial (100 Da, Ligand)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Nucleosomal core particle (Complex)
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Protein max (6 kDa, Protein from Homo sapiens)
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Histone h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Cmyc/max heterodimer (Complex from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8ajm
Q-score: 0.425
Pla-Prats C, Cavadini S, Kempf G, Thoma NH
EMBO J (2023) 42 pp. e112253-e112253 [ DOI: doi:10.15252/embj.2022112253 Pubmed: 36715408 ]
- T-complex protein 1 subunit epsilon (62 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Complex of ddb1-dcaf12-cct5 (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 12 (53 kDa, Protein from Homo sapiens)
Structure of the human DDB1-DCAF12 complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ajn
Q-score: 0.27
Pla-Prats C, Cavadini S, Kempf G, Thoma NH
EMBO J (2023) 42 pp. e112253-e112253 [ DOI: doi:10.15252/embj.2022112253 Pubmed: 36715408 ]
- Complex of ddb1-dcaf12 (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 12 (53 kDa, Protein from Homo sapiens)
Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5
Resolution: 30.6 Å
EM Method: Single-particle
Fitted PDBs: 8ajo
Q-score: 0.048
Pla-Prats C, Cavadini S, Kempf G, Thoma NH
EMBO J (2023) 42 pp. e112253-e112253 [ DOI: doi:10.15252/embj.2022112253 Pubmed: 36715408 ]
- T-complex protein 1 subunit epsilon (62 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Complex of ddb1-dcaf12-cct5 (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 12 (53 kDa, Protein from Homo sapiens)
Structure of the human CPLANE complex
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7q3d
Q-score: 0.327
Langousis G, Cavadini S, Boegholm N, Lorentzen E, Kempf G, Matthias P
Sci Adv (2022) 8 pp. eabn0832-eabn0832 [ DOI: doi:10.1126/sciadv.abn0832 Pubmed: 35427153 ]
- Wd repeat-containing and planar cell polarity effector protein fritz homolog (89 kDa, Protein from Homo sapiens)
- Cplane (Complex from Homo sapiens)
- Protein inturned (108 kDa, Protein from Homo sapiens)
- Protein fuzzy homolog (45 kDa, Protein from Homo sapiens)
Structure of the C9orf72-SMCR8 complex
Norpel J, Cavadini S, Schenk AD, Graff-Meyer A, Hess D, Seebacher J, Chao JA, Bhaskar V
PLoS Biol (2021) 19 pp. e3001344-e3001344 [ Pubmed: 34297726 DOI: doi:10.1371/journal.pbio.3001344 ]
- Guanine nucleotide exchange protein smcr8,guanine nucleotide exchange protein smcr8,maltose/maltodextrin-binding periplasmic protein (134 kDa, Protein from Escherichia coli K-12)
- C9orf72-smcr8 complex (201 kDa, Complex from Homo sapiens)
- Ubiquitin-like protein smt3,guanine nucleotide exchange c9orf72 (67 kDa, Protein from Homo sapiens)
Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 6y5e
Q-score: 0.43
Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A
Nature (2020) 587 pp. 668-672 [ Pubmed: 32911482 DOI: doi:10.1038/s41586-020-2750-6 ]
- Pentanedial (100 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (240 kDa, Complex)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
Nucleosome with OCT4-SOX2 motif at SHL-6
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 6t93
Q-score: 0.419
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH
Science (2020) 368 pp. 1460-1465 [ Pubmed: 32327602 DOI: doi:10.1126/science.abb0074 ]
- 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-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Cryo-EM structure of NCP-6-4PP
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6r93
Q-score: 0.352
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (45 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 6-4pp nucleosome (199 kDa, Complex)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
Cryo-EM structure of NCP_THF2(-3)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6r94
Q-score: 0.363
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Human dna (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 / 2a / 2b (Complex from Homo sapiens)
- Thf2 (-3) containing nucleosome (199 kDa, Complex)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)