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)
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
- Monomeric e6ap-e6-p53 ternary complex (176 kDa, Complex 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)
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
- Dimeric e6ap-e6-p53 ternary complex (352 kDa, Complex 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 ]
- Zinc ion (65 Da, Ligand)
- Dimer of ubr5 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ubr5 (313 kDa, Protein 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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Nucleosome-bound factors (Complex)
- Nucleosomal core particle (Complex)
- Myc-max and oct4-bound nucleosome (Complex)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Protein max (9 kDa, Protein from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Oct4 (Complex from Homo sapiens)
- Dna (127-mer) (39 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)
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 ]
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Cmyc/max heterodimer (Complex from Homo sapiens)
- Nucleosomal core particle (Complex)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Protein max (6 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
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 (14 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (Complex from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Cryo-em structure of cgas-ncp complex (240 kDa, Complex)
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 (Complex from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- 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)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein 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)
- Dna (Complex from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (240 kDa, Complex)
- 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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (146-mer) (46 kDa, DNA from synthetic construct)
- Pentanedial (100 Da, Ligand)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (70 kDa, Protein from Homo sapiens)
- G protein/gfp fusion protein,pou domain, class 5, transcription factor 1 (oct4) (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Sox2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Ternary complex of oct4-sox2 and shl-6 nucleosome (Complex)
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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (142-mer) (92 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Sox2 (Complex 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)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the BRISC complex bound to SHMT2
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6h3c
Q-score: 0.278
Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andres-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guerillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thoma NH
Mol Cell (2019) 75 pp. 483-497.e9 [ DOI: doi:10.1016/j.molcel.2019.06.002 Pubmed: 31253574 ]
- Shmt2 alpha (Complex from Homo sapiens)
- Lys-63-specific deubiquitinase brcc36 (38 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Brisc complex subunit abraxas 2 (49 kDa, Protein from Homo sapiens)
- Brisc and brca1-a complex member 2 (45 kDa, Protein from Homo sapiens)
- Brisc and brca1-a complex member 1 (39 kDa, Protein from Homo sapiens)
- Brisc complex bound to shmt2 alpha (438 kDa, Complex)
- Serine hydroxymethyltransferase, mitochondrial (56 kDa, Protein from Homo sapiens)
- Brisc complex (Complex from Homo sapiens)
- Water (18 Da, Ligand)