Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v4y
Q-score: 0.53
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ DOI: doi:10.1038/s41467-024-46178-y Pubmed: 38472177 ]
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Cryo-EM structure of doubly-bound SNF2h-nucleosome complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v6v
Q-score: 0.477
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ DOI: doi:10.1038/s41467-024-46178-y Pubmed: 38472177 ]
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8v7l
Q-score: 0.456
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ DOI: doi:10.1038/s41467-024-46178-y Pubmed: 38472177 ]
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 7cro
Q-score: 0.448
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd2 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd2 (79 kDa, Protein from Homo sapiens)
- Histone h3, h4, h2a and h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nsd2 bearing e1099k/t1150a dual mutation in complex with 187-bp ncp (300 kDa, Complex)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7crp
Q-score: 0.542
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd3 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Nsd3 bearing e1181k/t1232a dual mutation in complex with 187-bp ncp (1:1 binding mode) (300 kDa, Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7crq
Q-score: 0.507
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd3 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
- Nsd3 bearing e1181k/t1232a dual mutation in complex with 187-bp ncp (2:1 binding mode) (300 kDa, Complex)
Native NSD3 bound to 187-bp nucleosome
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 7crr
Q-score: 0.464
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Cryo-em structure of the native nsd3 bound to 187-bp nucleosome (300 kDa, Complex)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Dna(168-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Native nsd3 (Complex from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6ne3
Q-score: 0.42
Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y
eLife (2019) 8 [ Pubmed: 31210637 DOI: doi:10.7554/eLife.46057 ]
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (156-mer) (47 kDa, DNA from Xenopus laevis)
- Dna (156-mer) (48 kDa, DNA from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (54 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Cryo-em structure of singly-bound snf2h-nucleosome complex with snf2h bound at the flanking dna proximal side (340 MDa, Complex from Xenopus laevis)