7DBP: Histone H1.0

Linker histone defines structure and self-association behaviour of the 177 bp human chromosome. Determined by electron microscopy at 4.5 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 13,801
Mol. weight: 242 kDa
Released: 23 Dec 2020

Explore 7DBP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DBP contains 39 α-helices and 19 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.

Chain A: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-75	12
β-strand	83	1	2
α-helix	86-113	28
α-helix	121-131	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
α-helix	49-76	28
β-strand	80	1	2
α-helix	83-92	10
β-strand	96-97	2	3

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

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-36	9
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	100-101	2	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	36-45	10
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	89-98	10
α-helix	102-119	18

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
α-helix	121-131	11

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
α-helix	49-76	28
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-97	2	6

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-45	10
β-strand	50-51	2	9
α-helix	53-80	28
β-strand	85-86	2	8
α-helix	89-98	10
α-helix	102-119	18

Chain K: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
β-strand	25-26	2	1
α-helix	27-37	11
α-helix	42-45	4
α-helix	47-58	12
β-strand	61-63	3	1
β-strand	72-75	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H1.0	K	protein	211	Homo sapiens	P07305 (AlphaFold model)
Histone H3.1	A, E	protein	136	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	130	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	126	Homo sapiens	O60814
DNA (175-mer)	I	DNA	177	synthetic construct
DNA (175-mer)	J	DNA	177	synthetic construct

Sequence of entity 1 (K), FASTA

>7DBP_1 Histone H1.0 (chains K)
MHHHHHHSSGLEVLFQGPTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRA
GSSRQSIQKYIKSHYKVGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKK
SVAFKKTKKEIKKVATPKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTV
KAKPVKASKPKKAKPVKPKAKSSAKRAGKKK

Sequence of entity 2 (A, E), FASTA

>7DBP_2 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>7DBP_3 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>7DBP_4 Histone H2A type 1-B/E (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 5 (D, H), FASTA

>7DBP_5 Histone H2B type 1-K (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 6 (I), FASTA

>7DBP_6 DNA (175-MER) (chains I)
ACTTACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGC
TCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATT
ACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAAAGT

Sequence of entity 7 (J), FASTA

>7DBP_7 DNA (175-MER) (chains J)
ACTTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAAT
CCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCT
GTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTAAGT

Primary citation

Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Wang, S., Vogirala, V.K., Soman, A. et al. Sci Rep (2021) 11:380-380. DOI 10.1038/s41598-020-79654-8 · PubMed

Other PDB entries of the same protein (UniProt P07305 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7COW 2.86 Å, 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0
7K5X 2.93 Å, Cryo-EM structure of a chromatosome containing human linker histone H1.0
6LAB 3.2 Å, 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0
7XX6 3.39 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)
6LA8 3.4 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
7XVL 3.51 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)
30FM 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
30HD 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
6LA9 3.7 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0…
6LA2 3.89 Å, 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
8TB9 4.0 Å, PRC2-J119-450 monomer bound to H1-nucleosome
9IPU 4.3 Å, cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to…

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