Monomeric E6AP-E6-p53 ternary complex
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8r1f
Q-score: 0.316
Sandate CR, Chakraborty D, Kater L, Kempf G, Thoma NH
bioRxiv (2023) [ DOI: doi:10.1101/2023.11.01.565136 ]
- Zinc ion (65 Da, Ligand)
- Monomeric e6ap-e6-p53 ternary complex (176 kDa, Complex from Homo sapiens)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
Dimeric ternary structure of E6AP-E6-p53
Resolution: 3.99 Å
EM Method: Single-particle
Fitted PDBs: 8r1g
Q-score: 0.175
Sandate CR, Chakraborty D, Kater L, Kempf G, Thoma NH
bioRxiv (2023) [ DOI: doi:10.1101/2023.11.01.565136 ]
- Zinc ion (65 Da, Ligand)
- Dimeric e6ap-e6-p53 ternary complex (352 kDa, Complex from Homo sapiens)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
Cryo-EM structure of dimeric UBR5
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8p82
Q-score: 0.299
Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Slabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thoma NH, Ebert BL
Mol Cell (2023) 83 pp. 2753-2767.e10 [ DOI: doi:10.1016/j.molcel.2023.06.028 Pubmed: 37478846 ]
- E3 ubiquitin-protein ligase ubr5 (313 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dimer of ubr5 (Complex from Homo sapiens)
OCT4 and MYC-MAX co-bound to a nucleosome
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ots
Q-score: 0.404
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 proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Nucleosomal core particle (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Protein max (9 kDa, Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Oct4 (Complex from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Nucleosome-bound factors (Complex)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
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 ]
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Cmyc/max heterodimer (Complex from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Pentanedial (100 Da, Ligand)
- Nucleosomal core particle (Complex)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Protein max (6 kDa, Protein from Homo sapiens)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
Structure of human cGAS (K394E) bound to the nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6y5d
Q-score: 0.195
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 ]
- Histone h2a type 2-a (Complex from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Cryo-em structure of cgas-ncp complex (240 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Protein (Complex 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 ]
- Histone h4 (Complex from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (240 kDa, Complex)
- Dna (Complex from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
OCT4-SOX2-bound nucleosome - SHL-6
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 6t90
Q-score: 0.451
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 ]
- Pentanedial (100 Da, Ligand)
- Histones (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Ternary complex of oct4-sox2 and shl-6 nucleosome (Complex)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (70 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- G protein/gfp fusion protein,pou domain, class 5, transcription factor 1 (oct4) (Complex from Homo sapiens)
- Dna (146-mer) (46 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Sox2 (Complex from Homo sapiens)
OCT4-SOX2-bound nucleosome - SHL+6
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 6yov
Q-score: 0.35
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 ]
- Pentanedial (100 Da, Ligand)
- Histones (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Dna (Complex from synthetic construct)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (69 kDa, Protein from Homo sapiens)
- Dna (142-mer) (92 kDa, DNA from synthetic construct)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Sox2 (Complex from Homo sapiens)