5Z30: Histone H3.1

The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant. Determined by X-ray diffraction at 2.45 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,005
Mol. weight: 201.63 kDa
Ligands: MN
Released: 18 Jul 2018

Explore 5Z30 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z30 contains 40 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	121-130	10

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	19-23	5
α-helix	29-37	9
β-strand	45-46	2	4
α-helix	48-75	28
β-strand	80-81	2	5
α-helix	83-91	9
α-helix	94-99	6
β-strand	103-104	2	6
α-helix	115-117	3

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

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-122	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
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	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	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	83-92	10
β-strand	97-98	2	6

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	19-23	5
α-helix	29-38	10
β-strand	45-46	2	9
α-helix	50-74	25
β-strand	80-81	2	10
α-helix	83-91	9
α-helix	94-99	6
β-strand	103-104	2	3
α-helix	115-117	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	139	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	106	Homo sapiens	P62805 (AlphaFold model)
Histone H2A.Z	C, G	protein	131	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	129	Homo sapiens	P06899 (AlphaFold model)
DNA (146-mer)	I, J	DNA	146	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>5Z30_1 Histone H3.1 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5Z30_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5Z30_3 Histone H2A.Z (chains C, G)
GSHMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAA
ILEYLTAEVLELAGNASKDLKVKCITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKS
LIGKKGQQKTV

Sequence of entity 4 (D, H), FASTA

>5Z30_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK

Sequence of entity 5 (I, J), FASTA

>5Z30_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	11

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

Primary citation

Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Arimura, Y., Ikura, M., Fujita, R. et al. Nucleic Acids Res (2018) 46:10007-10018. DOI 10.1093/nar/gky661 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

Browse structure collections

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