6PWF: Histone H3

Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. Determined by electron microscopy at 4.07 Å resolution. Released 21 Aug 2019.

Method: Electron microscopy
Resolution: 4.07 Å
Organisms: Drosophila melanogaster, synthetic construct, Chaetomium thermophilum
Chains: 11
Atoms: 15,197
Mol. weight: 272.1 kDa
Released: 21 Aug 2019

Explore 6PWF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PWF contains 71 α-helices and 32 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and E: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	51-54	4
α-helix	64-74	11
α-helix	75-77	3
β-strand	83-84	2	1
α-helix	89-111	23
α-helix	112-114	3
β-strand	118-119	2	2
α-helix	121-132	12

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	32-40	9
β-strand	45-46	2	2
α-helix	50-61	12
α-helix	67-75	9
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96	1	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	29-34	6
β-strand	41-42	2	4
α-helix	46-66	21
α-helix	67-69	3
β-strand	76-77	2	5
α-helix	79-86	8
α-helix	92-95	4
β-strand	100	1	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-45	8
β-strand	50-51	2	5
α-helix	54-60	7
α-helix	67-80	14
β-strand	85-86	2	4
α-helix	89-96	8
α-helix	104-118	15

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-40	9
β-strand	45-46	2	8
α-helix	50-53	4
α-helix	55-61	7
α-helix	67-75	9
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97	1	6

Chain G: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-35	7
β-strand	42	1	9
α-helix	47-56	10
α-helix	61-64	4
α-helix	65-67	3
α-helix	79-88	10
α-helix	91-95	5
β-strand	99	1	3

Chain H: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	37-45	9
α-helix	53-81	29
β-strand	86	1	9
α-helix	104-111	8
α-helix	113-119	7

Chain K: 27 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	187-190	4
α-helix	194-202	9
β-strand	207-209	3	10
α-helix	218-224	7
α-helix	226	1
α-helix	227-231	5
β-strand	237-240	4	10
α-helix	243-245	3
α-helix	246-256	11
β-strand	262	1	10
α-helix	269-272	4
α-helix	274-277	4
β-strand	287-290	4	10
α-helix	292-296	5
β-strand	307-313	7	10
α-helix	317-319	3
α-helix	326-329	4
β-strand	334-341	8	10
α-helix	350-359	10
α-helix	364-367	4
α-helix	371-373	3
α-helix	381-385	5
α-helix	389-392	4
α-helix	401-403	3
β-strand	413	1	11
β-strand	418	1	12
α-helix	431-435	5
α-helix	454-459	6
α-helix	491-500	10
β-strand	508-510	3	11
α-helix	515-525	11
β-strand	532-534	3	11
α-helix	541-551	11
β-strand	560-562	3	11
β-strand	579-581	3	11
α-helix	591-594	4
α-helix	595-598	4
β-strand	609-611	3	11
β-strand	615	1	12
α-helix	620-629	10
α-helix	635-639	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	136	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	103	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G	protein	124	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	123	Drosophila melanogaster	P02283 (AlphaFold model)
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct
chromatin remodeling factor ISWI	K	protein	640	Chaetomium thermophilum	G0S9L5

Sequence of entity 1 (A, E), FASTA

>6PWF_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6PWF_2 Histone H4 (chains B, F)
MTGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6PWF_3 Histone H2A (chains C, G)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA

Sequence of entity 4 (D, H), FASTA

>6PWF_4 Histone H2B (chains D, H)
MPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK

Sequence of entity 5 (I), FASTA

>6PWF_5 DNA (147-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 6 (J), FASTA

>6PWF_6 DNA (147-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (K), FASTA

>6PWF_7 chromatin remodeling factor ISWI (chains K)
MAHHHHHHGHHHENLYFQGSSSGKKHDRLGENKEDDTLRRFRYLLGLTDLFRHFIETNPN
PKIREIMAEIDRQNAEEAKKGSSGGGSAETVFRESPPFIKGTMRDYQIAGLNWLISLHEN
GISGILADEMGLGKTLQTISFLGYLRHIQGITGPHLVAVPKSTLDNWKREFEKWTPDVNV
LVLQGAKEERHQLINDRLIDEDFDVCITSYEMILREKAHLKKFAWEYIIIDEAHRIKNEE
SSLSQVIRMFSSRNRLLITGTPLQNNLHELWALLNFLLPDVFGDSDAFDQWFRGQDRDQD
QVVQQLHRVLRPFLLRRVKSDVEKSLLPKKEINVYIGMSEMQVKWYKKILEKDIDAVNGA
GGKRESKTRLLNIVMQLRKCCNHPYLFEGAEPGPPYTTDEHLIYNSGKMIVLDKLLKRLQ
SQGSRVLIFSQMSRLLDILEDYCVFRGYKYCRIDGGTAHEDRIAAIDEYNRPGSDKFIFL
LTTRAGGLGINLTTADTVILYDSDWNPQADLQAMDRAHRIGQTKQVVVYRFVTDNAIEEK
VLERAAQKLRLDQLVIQQGRAQIATKAAANKEELLSMIQHGAEKVFQTKGAFGLMAEKGA
NLDDDDIDAILKAGEERTRELNAKYEKLGIDDLQKFTSES

Primary citation

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. Chittori, S., Hong, J., Bai, Y. et al. Nucleic Acids Res (2019) 47:9400-9409. DOI 10.1093/nar/gkz670 · PubMed

Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
2PYO 2.43 Å, Drosophila nucleosome core
8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3

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