5FUG: Human YL1-H2A.Z-H2B complex
Crystal structure of a human YL1-H2A.Z-H2B complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 Mar 2016.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organism
- HOMO SAPIENS
- Chains
- 12
- Atoms
- 7,175
- Mol. weight
- 120.75 kDa
- Released
- 9 Mar 2016
Explore 5FUG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5FUG contains 52 α-helices and 28 β-strands across 12 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 | 19-22 | 4 | |
| α-helix | 29-39 | 11 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 48-69 | 22 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-91 | 9 | |
| α-helix | 94-105 | 12 | |
Chains B and K: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 2 |
| β-strand | 55 | 1 | 3 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 1 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-121 | 18 | |
Chain C: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-22 | 6 | |
| α-helix | 29-32 | 4 | |
| α-helix | 33-35 | 3 | |
| β-strand | 45 | 1 | 3 |
| β-strand | 54-57 | 4 | 4 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 29-38 | 10 | |
| β-strand | 46 | 1 | 5 |
| α-helix | 48-70 | 23 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-91 | 9 | |
| α-helix | 94-105 | 12 | |
Chain E: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 6 |
| β-strand | 55 | 1 | 7 |
| α-helix | 56-83 | 28 | |
| β-strand | 89 | 1 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-23 | 7 | |
| α-helix | 28-31 | 4 | |
| α-helix | 44 | 1 | |
| β-strand | 45 | 1 | 7 |
| α-helix | 46 | 1 | |
| β-strand | 55-58 | 4 | 4 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 29-38 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 48-69 | 22 | |
| β-strand | 80-81 | 2 | 9 |
| α-helix | 83-91 | 9 | |
| α-helix | 94-102 | 9 | |
Chain H: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 9 |
| β-strand | 55 | 1 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
3 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 H2A.Z | A, D, G, J | protein | 110 | HOMO SAPIENS | P0C0S5 (AlphaFold model) |
| Histone H2B type 1-J | B, E, H, K | protein | 96 | HOMO SAPIENS | P06899 (AlphaFold model) |
| Vacuolar protein sorting-associated protein 72 homolog | C, F, I, L | protein | 68 | HOMO SAPIENS | Q15906 (AlphaFold model) |
Sequence of entity 1 (A, D, G, J), FASTA
>5FUG_1 HISTONE H2A.Z (chains A, D, G, J)
SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLK
VKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQKTV
Sequence of entity 2 (B, E, H, K), FASTA
>5FUG_2 HISTONE H2B TYPE 1-J (chains B, E, H, K)
KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 3 (C, F, I, L), FASTA
>5FUG_3 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG (chains C, F, I, L)
GSHMGRAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDF
DIDEGDEP
Primary citation
Molecular Basis and Specificity of H2A.Z-H2B Recognition and Deposition by the Histone Chaperone Yl1. Latrick, C.M., Marek, M., Ouararhni, K. et al. Nat Struct Mol Biol (2016) 23:309. DOI 10.1038/NSMB.3189 · PubMed
Other PDB entries of the same protein (UniProt P0C0S5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4CAY 1.48 Å, Crystal structure of a human Anp32e-H2A.Z-H2B complex
- 6KO2 1.5 Å, Crystal Structure of BRD4-Brmo2 in complex with H2A.ZK4acK7ac peptide
- 5CHL 1.89 Å, Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1…
- 9INC 2.01 Å, High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z…
- 6JOU 2.17 Å, Crystal structure of the human nucleosome containing H2A.Z.1 S42R
- 5B31 2.2 Å, The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1.
- 5B32 2.35 Å, The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3.
- 5Z30 2.45 Å, The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z…
- 9UBD 2.53 Å, The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP…
- 1F66 2.6 Å, 2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z
- 8T9F 2.6 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
- 4NFT 2.61 Å, Crystal structure of human lnkH2B-h2A.Z-Anp32e
Browse structure collections
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