2PYO: Drosophila nucleosome core

Drosophila nucleosome core. Determined by X-ray diffraction at 2.43 Å resolution. Released 6 Nov 2007.

Method: X-ray diffraction
Resolution: 2.43 Å
Organisms: Homo sapiens, Drosophila melanogaster
Chains: 10
Atoms: 12,239
Mol. weight: 197.82 kDa
Ligands: MN
Released: 6 Nov 2007

Explore 2PYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PYO contains 38 α-helices and 20 β-strands across 8 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.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
α-helix	26-35	10
β-strand	41-42	2	4
α-helix	45-71	27
β-strand	76-77	2	5
α-helix	79-88	10
α-helix	90-95	6
β-strand	100-101	2	6
α-helix	112-114	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-119	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-91	9
β-strand	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
α-helix	26-34	9
β-strand	41-42	2	9
α-helix	45-70	26
β-strand	76-77	2	10
α-helix	79-88	10
α-helix	90-95	6
β-strand	100-101	2	3
α-helix	112-114	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens
Histone H3	A, E	protein	135	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	102	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G	protein	120	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	122	Drosophila melanogaster	P02283 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>2PYO_1 DNA (147-MER) (chains I)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 2 (J), FASTA

>2PYO_2 DNA (147-MER) (chains J)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 3 (A, E), FASTA

>2PYO_3 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>2PYO_4 Histone H4 (chains B, F)
TGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>2PYO_5 Histone H2A (chains C, G)
SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE

Sequence of entity 6 (D, H), FASTA

>2PYO_6 Histone H2B (chains D, H)
PPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMN
SFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
SK

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	14

Water and common crystallization additives (CL) are not listed.

Primary citation

Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer. Clapier, C.R., Chakravarthy, S., Petosa, C. et al. Proteins (2007) 71:1-7. DOI 10.1002/prot.21720 · 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
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
2YBA 2.55 Å, Crystal structure of Nurf55 in complex with histone H3

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