9OGS: Cryo-EM analysis of human H2A.Z on Sat2R-P DNA
Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1). Determined by electron microscopy at 3.05 Å resolution. Released 5 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 3.05 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 11,117
- Mol. weight
- 202.21 kDa
- Released
- 5 Nov 2025
Explore 9OGS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9OGS contains 35 α-helices and 16 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 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 | 97-98 | 2 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-36 | 8 | |
| β-strand | 46 | 1 | 4 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-91 | 9 | |
| α-helix | 94-99 | 6 | |
| β-strand | 103-104 | 2 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| α-helix | 57-83 | 27 | |
| β-strand | 89 | 1 | 4 |
| α-helix | 91-99 | 9 | |
| α-helix | 105-122 | 18 | |
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 | 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 | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 5 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 30-36 | 7 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-91 | 9 | |
| α-helix | 94-99 | 6 | |
| β-strand | 103-104 | 2 | 3 |
Chain H: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 103 | 1 | |
| α-helix | 107-123 | 17 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.2 | A, E | protein | 136 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A.Z | C, G | protein | 127 | Homo sapiens | P0C0S5 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| Sat2R-P DNA (131-MER) | I, J | DNA | 152 | Homo sapiens | |
Sequence of entity 1 (A, E), FASTA
>9OGS_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9OGS_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9OGS_3 Histone H2A.Z (chains C, G)
AGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEY
LTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGK
KGQQKTV
Sequence of entity 4 (D, H), FASTA
>9OGS_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I, J), FASTA
>9OGS_5 Sat2R-P DNA (131-MER) (chains I, J)
ATCATCAGATTCCATTCGAATCCATTCGAAAATGATTACATTCGAATCCATTCGAAGATT
CCATTTGAGCCTGCTCGAGCAGGCTCAAATGGAATCTTCGAATGGATTCGAATGTAATCA
TTTTCGAATGGATTCGAATGGAATCTGATGAT
Primary citation
Impacts of DNA methylation on H2A.Z deposition and nucleosome stability. Shih, R.M., Arimura, Y., Konishi, H.A. et al. Elife (2026) 15. DOI 10.7554/eLife.109762 · 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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