2X4X: Peregrin
Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. Determined by X-ray diffraction at 1.85 Å resolution. Released 21 Apr 2010.
- Method
- X-ray diffraction
- Resolution
- 1.85 Å
- Organism
- HOMO SAPIENS
- Chains
- 8
- Atoms
- 5,028
- Mol. weight
- 70.42 kDa
- Released
- 21 Apr 2010
Explore 2X4X in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2X4X contains 31 α-helices and 32 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: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1088-1091 | 4 | 1 |
| α-helix | 1097-1098 | 2 | |
| β-strand | 1099-1104 | 6 | 1 |
| β-strand | 1113-1115 | 3 | 2 |
| β-strand | 1118-1120 | 3 | 2 |
| α-helix | 1121-1124 | 4 | |
| α-helix | 1125-1138 | 14 | |
| β-strand | 1142-1147 | 6 | 1 |
| β-strand | 1154-1158 | 5 | 1 |
| α-helix | 1159-1161 | 3 | |
| β-strand | 1162-1164 | 3 | 1 |
| α-helix | 1169-1176 | 8 | |
| α-helix | 1182-1202 | 21 | |
Chain B: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-31 | 3 | |
| β-strand | 35 | 1 | 1 |
| α-helix | 36-39 | 4 | |
Chain C: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1088-1091 | 4 | 3 |
| α-helix | 1097-1098 | 2 | |
| β-strand | 1099-1104 | 6 | 3 |
| β-strand | 1113-1115 | 3 | 4 |
| β-strand | 1118-1120 | 3 | 4 |
| α-helix | 1121-1124 | 4 | |
| α-helix | 1125-1138 | 14 | |
| β-strand | 1142-1147 | 6 | 3 |
| β-strand | 1154-1158 | 5 | 3 |
| α-helix | 1159-1161 | 3 | |
| β-strand | 1162-1164 | 3 | 3 |
| α-helix | 1169-1176 | 8 | |
| α-helix | 1182-1203 | 22 | |
Chains D and H: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-31 | 3 | |
| β-strand | 35 | 1 | 3 |
| α-helix | 36-38 | 3 | |
Chain E: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1081-1083 | 3 | |
| β-strand | 1088-1091 | 4 | 5 |
| β-strand | 1099-1104 | 6 | 5 |
| β-strand | 1113-1115 | 3 | 6 |
| β-strand | 1118-1120 | 3 | 6 |
| α-helix | 1121-1124 | 4 | |
| α-helix | 1125-1138 | 14 | |
| β-strand | 1143-1147 | 5 | 5 |
| β-strand | 1154-1157 | 4 | 5 |
| α-helix | 1159-1161 | 3 | |
| β-strand | 1162-1164 | 3 | 5 |
| α-helix | 1169-1176 | 8 | |
| α-helix | 1182-1203 | 22 | |
Chain F: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-31 | 3 | |
| β-strand | 35 | 1 | 5 |
Chain G: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1088-1091 | 4 | 7 |
| α-helix | 1097-1098 | 2 | |
| β-strand | 1099-1104 | 6 | 7 |
| β-strand | 1114-1115 | 2 | 8 |
| β-strand | 1118-1119 | 2 | 8 |
| α-helix | 1121-1124 | 4 | |
| α-helix | 1125-1138 | 14 | |
| β-strand | 1142-1147 | 6 | 7 |
| β-strand | 1154-1158 | 5 | 7 |
| α-helix | 1159-1161 | 3 | |
| β-strand | 1162-1164 | 3 | 7 |
| α-helix | 1169-1176 | 8 | |
| α-helix | 1182-1202 | 21 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Peregrin | A, C, E, G | protein | 132 | HOMO SAPIENS | P55201 (AlphaFold model) |
| Histone H3.2 | B, D, F, H | protein | 21 | HOMO SAPIENS | Q71DI3 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>2X4X_1 PEREGRIN (chains A, C, E, G)
GGSEDEDSPLDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQ
MTQEAREHLYLVLFFDNKRTWQWLPRTKLVPLGVNQDLDKEKMLEGRKSNIRKSVQIAYH
RALQHRSKVQGE
Sequence of entity 2 (B, D, F, H), FASTA
>2X4X_2 HISTONE H3.2 (chains B, D, F, H)
TKAARKSAPATGGVKKPHRYR
Primary citation
Molecular Basis of Histone H3K36Me3 Recognition by the Pwwp Domain of Brpf1. Vezzoli, A., Bonadies, N., Allen, M.D. et al. Nat Struct Mol Biol (2010) 17:617. DOI 10.1038/NSMB.1797 · PubMed
Other PDB entries of the same protein (UniProt P55201 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5MWZ 1.25 Å, Crystal structure of the human BRPF1 bromodomain in complex with BZ073
- 3L42 1.3 Å, PWWP domain of human bromodomain and PHD finger containing protein 1
- 5C6S 1.3 Å, Human Bromodomain and PHD Finger Containing 1, PWWP domain in complex with XST005904a
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 5O5F 1.3 Å, Crystal structure of the human BRPF1 bromodomain in complex with BZ038
- 5ETB 1.33 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED13
- 5D7X 1.35 Å, Crystal structure of the human BRPF1 bromodomain in complex with XZ08
- 7C4I 1.37 Å, High resolution structure of BRPF1 Bromo Domain from Biortus
- 5EM3 1.4 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED9
- 5ETD 1.4 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED14
- 8QAZ 1.4 Å, Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative…
- 8QB2 1.42 Å, Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative…
Browse structure collections
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