6IPU: Histone H3.1

Human nucleosome core particle containing 145 bp of DNA. Determined by X-ray diffraction at 1.99 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,177
Mol. weight: 176.89 kDa
Ligands: MN
Released: 15 Jan 2020

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

Secondary structure: helices and β-sheets

6IPU contains 39 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	96-98	3	3

Chain C: 6 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	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain D: 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	101-120	20

Chain E: 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	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	19-22	4
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	96-98	3	6

Chain G: 6 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	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain H: 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	101-119	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	98	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B	protein	82	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	107	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	95	Homo sapiens	P06899 (AlphaFold model)
Histone H4	F	protein	87	Homo sapiens	P62805 (AlphaFold model)
DNA (145-mer)	I	DNA	145	Homo sapiens
DNA (145-mer)	J	DNA	145	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>6IPU_1 Histone H3.1 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>6IPU_2 Histone H4 (chains B)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6IPU_3 Histone H2A type 1-B/E (chains C, G)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK

Sequence of entity 4 (D, H), FASTA

>6IPU_4 Histone H2B type 1-J (chains D, H)
RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 5 (F), FASTA

>6IPU_5 Histone H4 (chains F)
KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH
AKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (I), FASTA

>6IPU_6 DNA (145-MER) (chains I)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 7 (J), FASTA

>6IPU_7 DNA (145-MER) (chains J)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	5

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

Primary citation

PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome. Sharma, D., De Falco, L., Padavattan, S. et al. Nat Commun (2019) 10:5751-5751. DOI 10.1038/s41467-019-13641-0 · 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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