3WA9: The nucleosome containing human H2A.Z.1
The nucleosome containing human H2A.Z.1. Determined by X-ray diffraction at 3.07 Å resolution. Released 18 Dec 2013.
- Method
- X-ray diffraction
- Resolution
- 3.07 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 11,925
- Mol. weight
- 201.06 kDa
- Released
- 18 Dec 2013
Explore 3WA9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3WA9 contains 40 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 | 64-76 | 13 | |
| 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 | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| 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 | 19-23 | 5 | |
| α-helix | 29-37 | 9 | |
| β-strand | 45-46 | 2 | 4 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 5 |
| α-helix | 83-92 | 10 | |
| α-helix | 94-99 | 6 | |
| β-strand | 103-104 | 2 | 6 |
| α-helix | 115-117 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-99 | 9 | |
| α-helix | 104-122 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
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 | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-36 | 8 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 50-74 | 25 | |
| β-strand | 80-81 | 2 | 10 |
| α-helix | 82 | 1 | |
| α-helix | 83-91 | 9 | |
| α-helix | 94-99 | 6 | |
| β-strand | 103-104 | 2 | 3 |
| α-helix | 115-117 | 3 | |
Chain H: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 103 | 1 | |
| α-helix | 106-123 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 139 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A.Z | C, G | protein | 131 | Homo sapiens | P0C0S5 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 129 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (146-mer) | I, J | DNA | 146 | | |
Sequence of entity 1 (A, E), FASTA
>3WA9_1 Histone H3.1 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>3WA9_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>3WA9_3 Histone H2A.Z (chains C, G)
GSHMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAA
ILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKS
LIGKKGQQKTV
Sequence of entity 4 (D, H), FASTA
>3WA9_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK
Sequence of entity 5 (I, J), FASTA
>3WA9_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Primary citation
Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2. Horikoshi, N., Sato, K., Shimada, K. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:2431-2439. DOI 10.1107/S090744491302252X · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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