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Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H
Nano Letters (2024) 24 pp. 5031-5038 [ DOI: doi:10.1021/acs.nanolett.4c00915 Pubmed: 38602296 ]
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 dna (Complex from synthetic construct)
- Nucleosomal core particle (Complex from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex from Homo sapiens)
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 ]
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Nucleosome core particle (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
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 ]
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Cryo-em structure of cgas-ncp complex (240 kDa, Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (Complex from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Structure of human cGAS bound to the nucleosome (focused refinement of cGAS-NCP subcomplex)
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 h2b type 1-k (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Cyclic gmp-amp synthase (Protein from Homo sapiens)
- Histone h2a type 2-c (Protein from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (240 kDa, Complex)
- Dna (153-mer) (RNA from Homo sapiens)
- Histone h3.2 (Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (Complex from Homo sapiens)
- Dna (153-mer) (Protein from Homo sapiens)
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6r8y
Q-score: 0.313
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Uv-ddb bound to a 6-4pp containing nucleosome (199 kDa, Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna damage-binding proteins (Complex from Homo sapiens)
- Histones (Complex from Homo sapiens)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6r90
Q-score: 0.278
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h4 (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome class a (199 kDa, Complex)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
Cryo-EM structure of NCP_THF2(-3)-UV-DDB
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6r91
Q-score: 0.212
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h4 (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 (-3) containing nucleosome (Complex)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6r92
Q-score: 0.22
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h4 (Complex from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1,dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Uv-ddb bound to a thf2 (+1) containing nucleosome class b (Complex)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA 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)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h4 (Complex 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)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- 6-4pp nucleosome (199 kDa, Complex)