6WAT: Complex structure of PHF1
complex structure of PHF1. Determined by X-ray diffraction at 1.8 Å resolution. Released 26 Aug 2020.
- Method
- X-ray diffraction
- Resolution
- 1.8 Å
- Organism
- Homo sapiens
- Chains
- 60
- Atoms
- 16,435
- Mol. weight
- 238.71 kDa
- Released
- 26 Aug 2020
Explore 6WAT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6WAT contains 33 α-helices and 240 β-strands across 60 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.
Chains a, A, B, c, C, d, f, g, H, J, M, N, P, Q, S, T, Y and Z: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-23 | 2 | 41 |
| β-strand | 24-25 | 2 | 42 |
Chains AA, BA, CA, EA, EC, FA, FC, GA, HA, KA, MC and NC: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-40 | 5 | 1 |
| β-strand | 46-55 | 10 | 1 |
| β-strand | 60-65 | 6 | 1 |
| β-strand | 70-74 | 5 | 1 |
| α-helix | 75-77 | 3 | |
| β-strand | 78-79 | 2 | 1 |
| β-strand | 81-84 | 4 | 2 |
Chains AC, BC, CC and IC: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-40 | 5 | 5 |
| β-strand | 46-55 | 10 | 5 |
| β-strand | 60-64 | 5 | 5 |
| β-strand | 70-74 | 5 | 5 |
| α-helix | 75-77 | 3 | |
| β-strand | 78-79 | 2 | 5 |
| β-strand | 81-85 | 5 | 2 |
Chains b, D, e, F, G, I, L, R and V: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-23 | 2 | 44 |
| β-strand | 24 | 1 | 43 |
Chains DA and GC: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-40 | 5 | 16 |
| β-strand | 46-55 | 10 | 16 |
| β-strand | 60-64 | 5 | 16 |
| β-strand | 70-74 | 5 | 16 |
| α-helix | 75-77 | 3 | |
| β-strand | 78-79 | 2 | 16 |
| β-strand | 81-84 | 4 | 17 |
Chains DC, HC, IA, JA, JC, KC, LA, LC, MA, NA, OA and OC: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-40 | 5 | 18 |
| β-strand | 46-55 | 10 | 18 |
| β-strand | 60-65 | 6 | 18 |
| β-strand | 70-74 | 5 | 18 |
| α-helix | 75-77 | 3 | |
| β-strand | 78-79 | 2 | 18 |
| β-strand | 81-85 | 5 | 17 |
Chains E, K and O: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-23 | 2 | 14 |
| β-strand | 24-25 | 2 | 13 |
| α-helix | 26-28 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| PHD finger protein 1 | AA, AC, BA, BC, CA, CC, DA, DC, EA, EC, FA, FC, GA, GC, HA, HC, IA, IC, JA, JC, KA, KC, LA, LC, MA, MC, NA, NC, OA, OC | protein | 61 | Homo sapiens | O43189 (AlphaFold model) |
| Histone H3.1t peptide | A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, Y, Z, a, b, c, d, e, f, g | protein | 9 | Homo sapiens | Q16695 (AlphaFold model) |
Sequence of entity 1 (AA, AC, BA, BC, CA, CC, DA, DC, EA, EC, FA, FC, GA, GC, HA, HC, IA, IC, JA, JC, KA, KC, LA, LC, MA, MC, NA, NC, OA, OC), FASTA
>6WAT_1 PHD finger protein 1 (chains AA, AC, BA, BC, CA, CC, DA, DC, EA, EC, FA, FC, GA, GC, HA, HC, IA, IC, JA, JC, KA, KC, LA, LC, MA, MC, NA, NC, OA, OC)
GRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALPGE
E
Sequence of entity 2 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, Y, Z, a, b, c, d, e, f, g), FASTA
>6WAT_2 Histone H3.1t peptide (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, Y, Z, a, b, c, d, e, f, g)
ATKVARKSA
Primary citation
Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Dong, C., Nakagawa, R., Oyama, K. et al. Elife (2020) 9. DOI 10.7554/eLife.58675 · PubMed
Other PDB entries of the same protein (UniProt O43189 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6WAV 1.7 Å, Crystal structure of PHF1 in complex with H3K36me3 substitution
- 4HCZ 1.85 Å, PHF1 Tudor in complex with H3K36me3
- 7LKY 1.85 Å, Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
- 5XFN 1.9 Å, Structure of the N-terminal domains of PHF1
- 5XFO 1.9 Å, Structure of the N-terminal domains of PHF1
- 5XFP 2.3 Å, Binary complex of PHF1 and a double stranded DNA
- 8H43 2.3 Å, Crystal structure of PHF1 Tudor domain in complex with hit 1
- 2E5P Solution structure of the TUDOR domain of PHD finger protein 1 (PHF1 protein)
- 2M0O The solution structure of human PHF1 in complex with H3K36me3
Browse structure collections
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