9NQU: Histone H3.2
KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate. Determined by electron microscopy at 3.16 Å resolution. Released 23 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 3.16 Å
- Organisms
- Homo sapiens, synthetic construct, Mus musculus
- Chains
- 11
- Atoms
- 17,358
- Mol. weight
- 281.32 kDa
- Ligands
- ZN, FE, OH0
- Released
- 23 Jul 2025
Explore 9NQU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9NQU contains 56 α-helices and 46 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-129 | 9 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-25 | 3 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 5 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 46-71 | 26 | |
| β-strand | 78 | 1 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 9 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.2 | A, E | protein | 135 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1 | C, G | protein | 129 | Homo sapiens | P0C0S8 (AlphaFold model) |
| Histone H2B type 1-C/E/F/G/I | D, H | protein | 125 | Homo sapiens | P62807 (AlphaFold model) |
| DNA (185-mer) | I | DNA | 185 | synthetic construct | |
| DNA (185-mer) | J | DNA | 185 | synthetic construct | |
| Lysine-specific demethylase 6B | K | protein | 514 | Mus musculus | Q5NCY0 |
Sequence of entity 1 (A, E), FASTA
>9NQU_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARCSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9NQU_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9NQU_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>9NQU_4 Histone H2B type 1-C/E/F/G/I (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Sequence of entity 5 (I), FASTA
>9NQU_5 DNA (185-MER) (chains I)
ATCCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGA
CAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGG
GATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACA
GCGAT
Sequence of entity 6 (J), FASTA
>9NQU_6 DNA (185-MER) (chains J)
ATCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAG
TAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAG
AGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTATA
GGGAT
Sequence of entity 7 (K), FASTA
>9NQU_7 Lysine-specific demethylase 6B (chains K)
GSDLTISHCAADVMRASKNAKVKGKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPSIY
LESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQV
QQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEERESEDEESEEPDST
TGTSPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHT
ILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHG
VDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLT
AYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQV
QRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRR
SAGLQGVVVLEQYRTEELAQAYDAFTLAPASTSR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| FE | FE (III) ion | Fe | 1 |
| OH0 | N-heptanoyl-N-hydroxy-beta-alanine | C10 H19 N O4 | 1 |
Primary citation
Structural mechanism of H3K27 demethylation and crosstalk with heterochromatin markers. Lin, C.C., Zhao, Y., Foley, C.A. et al. Mol Cell (2025) 85:2869-2884.e6. DOI 10.1016/j.molcel.2025.06.025 · PubMed
Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
- 2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
- 5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
- 6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- 7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
- 4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
- 4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Browse structure collections
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