9QIK: M2 nucleosome

M2 nucleosome. Determined by electron microscopy at 3.03 Å resolution. Released 21 Jan 2026.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Xenopus laevis laevis, Xenopus laevis
Chains: 10
Atoms: 10,927
Mol. weight: 245.29 kDa
Released: 21 Jan 2026

Explore 9QIK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QIK 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-37	10
β-strand	43-44	2	1
α-helix	48-73	26
β-strand	78-79	2	2
α-helix	81-89	9
α-helix	92-97	6
β-strand	102-103	2	3

Chain B: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	18-22	5
α-helix	28-37	10
β-strand	43-44	2	4
α-helix	47-73	27
β-strand	78-79	2	5
α-helix	80	1
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	6

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	2
α-helix	57-84	28
β-strand	89-90	2	1
α-helix	92-102	11
α-helix	105-124	20

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-85	29
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	105-123	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	46-57	12
α-helix	65-79	15
β-strand	84-85	2	7
α-helix	87-114	28
β-strand	119-120	2	8
α-helix	122-132	11

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	65-79	15
β-strand	84-85	2	9
α-helix	87-114	28
β-strand	119-120	2	10
α-helix	122-132	11

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
α-helix	32-41	10
β-strand	46-47	2	8
α-helix	51-76	26
β-strand	81-82	2	7
α-helix	83	1
α-helix	84-94	11
β-strand	98-99	2	3

Chain H: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-41	10
β-strand	46-47	2	10
α-helix	51-76	26
β-strand	81-82	2	9
α-helix	84-94	11
β-strand	98-99	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A type 1	A, B	protein	130	Xenopus laevis laevis	P06897 (AlphaFold model)
Histone H2B 1.1	C, D	protein	126	Xenopus laevis laevis	P02281 (AlphaFold model)
Histone H3	E, F	protein	136	Xenopus laevis	A0A8T2P505 (AlphaFold model)
Histone H4	G, H	protein	103	Xenopus laevis laevis	A0A8J1LTD2 (AlphaFold model)
DNA (220-mer)	I	DNA	220	Xenopus laevis laevis
DNA (220-mer)	J	DNA	220	Xenopus laevis laevis

Sequence of entity 1 (A, B), FASTA

>9QIK_1 Histone H2A type 1 (chains A, B)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK
TESAKSAKSK

Sequence of entity 2 (C, D), FASTA

>9QIK_2 Histone H2B 1.1 (chains C, D)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 3 (E, F), FASTA

>9QIK_3 Histone H3 (chains E, F)
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (G, H), FASTA

>9QIK_4 Histone H4 (chains G, H)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (I), FASTA

>9QIK_5 DNA (220-MER) (chains I)
TTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACTCGGGTTC
AATACATGCATGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGGGAGTAATCCCCTT
GGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTAC
TAGTCTCCAGGCACGTGTCAGATATATACATCCTGGGGCG

Sequence of entity 6 (J), FASTA

>9QIK_6 DNA (220-MER) (chains J)
CGCCCCAGGATGTATATATCTGACACGTGCCTGGAGACTAGTAGCAAGCTCTAGCACCGC
TTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCGACCA
ATTGAGCGGCCTCGGCACCGGGATTCTCCATGCATGTATTGAACCCGAGTACCGAGCTCG
AATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAA

Primary citation

DNA bendability inside the nucleosome regulates INO80's nucleosome positioning. Shukla, S., Ngubo, M., Paul, S. et al. Mol Cell (2025) 85:4318-4332.e9. DOI 10.1016/j.molcel.2025.10.010 · PubMed

Other PDB entries of the same protein (UniProt P06897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W4L 1.31 Å, The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis
8ZVY 1.72 Å, Alpha-Synuclein with H2a-H2b dimer complex structure.
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1P3I 2.3 Å, Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

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