6FQ8: Class 3 : translocated nucleosome

Class 3 : translocated nucleosome. Determined by electron microscopy at 4.8 Å resolution. Released 18 Apr 2018.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Xenopus laevis, synthetic construct
Chains: 10
Atoms: 11,913
Mol. weight: 179.03 kDa
Released: 18 Apr 2018

Explore 6FQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FQ8 contains 37 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	64-75	12
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	25-28	4
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	48-76	29
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	17-20	4
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	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	101-119	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	48-75	28
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	46-71	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	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	101-120	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3C	A, E	protein	98	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	B, F	protein	86	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	110	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	95	Xenopus laevis	P02281 (AlphaFold model)
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct

Sequence of entity 1 (A, E), FASTA

>6FQ8_1 Histone H3.3C (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

Sequence of entity 2 (B, F), FASTA

>6FQ8_2 Histone H4 (chains B, F)
RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA
KRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6FQ8_3 Histone H2A (chains C, G)
KTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGN
AARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Sequence of entity 4 (D, H), FASTA

>6FQ8_4 Histone H2B (chains D, H)
RKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 5 (I), FASTA

>6FQ8_5 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 6 (J), FASTA

>6FQ8_6 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Primary citation

Structural rearrangements of the histone octamer translocate DNA. Bilokapic, S., Strauss, M., Halic, M. Nat Commun (2018) 9:1330-1330. DOI 10.1038/s41467-018-03677-z · PubMed

Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1AOI 2.8 Å, Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment
8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
6PX1 3.3 Å, Set2 bound to nucleosome
8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
6NZO 3.8 Å, Set2 bound to nucleosome

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