5WCU: 167 bp nucleosome

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5. Determined by X-ray diffraction at 5.53 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 5.53 Å
Organisms: Drosophila melanogaster, synthetic construct, Gallus gallus
Chains: 22
Atoms: 26,619
Mol. weight: 393.47 kDa
Released: 31 Oct 2018

Explore 5WCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WCU contains 79 α-helices and 45 β-strands across 18 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chains B, F and L: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	78	1	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	51	1	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-120	20

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chains G and Q: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3

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

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-120	20

Chains K and O: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	11
α-helix	86-113	28
β-strand	118-119	2	12
α-helix	121-131	11

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E, K, O	protein	98	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F, L, P	protein	82	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G, M, Q	protein	104	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H, N, R	protein	94	Drosophila melanogaster	P02283 (AlphaFold model)
DNA (167-mer)	I, S	DNA	167	synthetic construct
DNA (167-mer)	J, T	DNA	167	synthetic construct
Histone H5	U, V	protein	76	Gallus gallus	P02259

Sequence of entity 1 (A, E, K, O), FASTA

>5WCU_1 Histone H3 (chains A, E, K, O)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F, L, P), FASTA

>5WCU_2 Histone H4 (chains B, F, L, P)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G, M, Q), FASTA

>5WCU_3 Histone H2A (chains C, G, M, Q)
KSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK
KTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPK

Sequence of entity 4 (D, H, N, R), FASTA

>5WCU_4 Histone H2B (chains D, H, N, R)
RKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Sequence of entity 5 (I, S), FASTA

>5WCU_5 DNA (167-MER) (chains I, S)
ATCGGCCGCCATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCGATGCATGTAGAT

Sequence of entity 6 (J, T), FASTA

>5WCU_6 DNA (167-MER) (chains J, T)
ATCTACATGCATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATGGCGGCCGAT

Sequence of entity 7 (U, V), FASTA

>5WCU_7 Histone H5 (chains U, V)
SASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVL
KQTKGVGASGSFRLAK

Primary citation

Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. Zhou, B.R., Jiang, J., Ghirlando, R. et al. J Mol Biol (2018) 430:3093-3110. DOI 10.1016/j.jmb.2018.06.020 · 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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