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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
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 ]
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Nucleosomal core particle (Complex)
- Dna (124-mer) (46 kDa, DNA from synthetic construct)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Nucleosomal core particle (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 1)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosomal core particle (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone octamer (Complex from Homo sapiens)
- Protein max (9 kDa, Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Oct4 (Complex from Homo sapiens)
- Nucleosome-bound factors (Complex)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Nucleosomal core particle (Complex)
- Cmyc/max heterodimer (Complex from Homo sapiens)
- Histone h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Histone octamer (Complex 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)
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
CryoEM Structure of cGAS Nucleosome complex
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7a08
Q-score: 0.533
Michalski S, de Oliveira Mann CC, Stafford CA, Witte G, Bartho J, Lammens K, Hornung V, Hopfner KP
Nature (2020) 587 pp. 678-682 [ DOI: doi:10.1038/s41586-020-2748-0 Pubmed: 32911480 ]
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (43 kDa, Protein from Mus musculus)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nucleosome (Complex from Homo sapiens)
- Cgas (Complex from Mus musculus)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosomal dna strand 1 (45 kDa, DNA from synthetic construct)
- Cgas, nucleosome and dna (Complex)
- Nucleosomal dna strands 1 and 2 (Complex from synthetic construct)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Nucleosomal dna strand 2 (45 kDa, DNA from synthetic construct)
CryoEM Structure INO80core Nucleosome complex
Resolution: 4.34 Å
EM Method: Single-particle
Fitted PDBs: 6fml
Q-score: 0.33
Eustermann S, Schall K, Kostrewa D, Lakomek K, Strauss M, Moldt M, Hopfner KP
Nature (2018) 556 pp. 386-390 [ Pubmed: 29643509 DOI: doi:10.1038/s41586-018-0029-y ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Ies6 (23 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Nucleosomal dna strand 1 (60 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Ino80core nucleosome complex (1 MDa, Complex)
- Les2 (52 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Ino80 (210 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Synthetic deoxyribonucleic acid (Complex from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Histone octamer (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Ino80core (Complex from Chaetomium thermophilum var. thermophilum DSM 1495)
- Ruvb-like helicase (50 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Nucleosomal dna strand 2 (60 kDa, DNA from synthetic construct)
- Actin related protein 5 (85 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Ruvb-like helicase (53 kDa, Protein from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))