Negative stain map of UBR5 (dimer) in complex with RARA/RXRA
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 [ Pubmed: 37478846 DOI: doi:10.1016/j.molcel.2023.06.028 ]
- Rxra (Protein from Homo sapiens)
- Rara (Protein from Homo sapiens)
- Ubr5 in complex with rara/rxra (Complex from Homo sapiens)
- Ubr5 (Protein from Homo sapiens)
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 8osj
Q-score: 0.219
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 ]
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8osk
Q-score: 0.267
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)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (124-mer) (46 kDa, DNA from synthetic construct)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal core particle (Complex)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 8osl
Q-score: 0.177
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 ]
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
MAX-MAX bound to a nucleosome at SHL+5.1 and SHL-6.9.
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 ]
- Max-max bound to a nucleosome at shl+5.1 and shl-6.9 (Complex)
- Histone h4 (Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Max (Complex from Homo sapiens)
- Histone h2b type 1-j (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Dna (127-mer) (DNA from synthetic construct)
- Histone h3.1 (Protein from Homo sapiens)
- Max (Protein from Homo sapiens)
- Histones (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 ]
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Nucleosome-bound factors (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Nucleosomal core particle (Complex)
- Histone octamer (Complex from Homo sapiens)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Protein max (9 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Oct4 (Complex 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 h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Protein max (6 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Nucleosomal dna (Complex from synthetic construct)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
- Nucleosomal core particle (Complex)
- Histone octamer (Complex from Homo sapiens)
- Cmyc/max heterodimer (Complex 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 ]
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Complex of ddb1-dcaf12 (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 ]
- Cplane (Complex from Homo sapiens)
- Protein fuzzy homolog (45 kDa, Protein from Homo sapiens)
- Protein inturned (108 kDa, Protein from Homo sapiens)
- Wd repeat-containing and planar cell polarity effector protein fritz homolog (89 kDa, Protein from Homo sapiens)
Structure of the mouse CPLANE-RSG1 complex
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7q3e
Q-score: 0.389
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 ]
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Protein fuzzy homolog (45 kDa, Protein from Mus musculus)
- Ciliogenesis and planar polarity effector 2 (28 kDa, Protein from Mus musculus)
- Wd repeat-containing and planar cell polarity effector protein fritz homolog (86 kDa, Protein from Mus musculus)
- Protein inturned (107 kDa, Protein from Mus musculus)
- Cplane complex (Complex from Mus musculus)