Structure of PHF8 in complex with histone H3. Determined by X-ray diffraction at 2.19 Å resolution. Released 22 Dec 2009.
Explore 3KV4 in 3D Show helices and sheets RCSB PDB PDBe
3KV4 contains 25 α-helices and 23 β-strands across 2 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 6-7 | 2 | 1 |
| β-strand | 12-13 | 2 | 1 |
| β-strand | 20-22 | 3 | 2 |
| β-strand | 29-31 | 3 | 2 |
| α-helix | 32-35 | 4 | |
| α-helix | 39-42 | 4 | |
| β-strand | 45-47 | 3 | 3 |
| α-helix | 51-57 | 7 | |
| β-strand | 61-62 | 2 | 3 |
| α-helix | 79-81 | 3 | |
| α-helix | 85-92 | 8 | |
| β-strand | 97-98 | 2 | 4 |
| α-helix | 99-101 | 3 | |
| β-strand | 104 | 1 | 5 |
| α-helix | 113-118 | 6 | |
| β-strand | 125-127 | 3 | 5 |
| β-strand | 136 | 1 | 6 |
| α-helix | 144-151 | 8 | |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 166-171 | 6 | 5 |
| α-helix | 172-180 | 9 | |
| β-strand | 188-194 | 7 | 5 |
| α-helix | 199-203 | 5 | |
| β-strand | 205 | 1 | 6 |
| α-helix | 208-213 | 6 | |
| α-helix | 215-219 | 5 | |
| α-helix | 227-229 | 3 | |
| β-strand | 234-238 | 5 | 5 |
| β-strand | 242-247 | 6 | 4 |
| α-helix | 250-252 | 3 | |
| β-strand | 254-261 | 8 | 5 |
| β-strand | 263-269 | 7 | 4 |
| α-helix | 273-283 | 11 | |
| α-helix | 288-290 | 3 | |
| α-helix | 293-296 | 4 | |
| β-strand | 301-306 | 6 | 4 |
| β-strand | 310-313 | 4 | 5 |
| α-helix | 314 | 1 | |
| β-strand | 318-323 | 6 | 4 |
| β-strand | 327-334 | 8 | 5 |
| α-helix | 340-352 | 13 | |
| α-helix | 357-359 | 3 | |
| α-helix | 364-384 | 21 | |
| α-helix | 391-407 | 17 | |
| α-helix | 413-415 | 3 | |
| α-helix | 417-419 | 3 | |
| α-helix | 426-446 | 21 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| PHD finger protein 8 | A | protein | 447 | Homo sapiens | Q9UPP1 (AlphaFold model) |
| Histone H3-like | B | protein | 24 | Q6NXT2 (AlphaFold model) |
>3KV4_1 PHD finger protein 8 (chains A) MASVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPS IMKKRRGSSKGHDTHKGKPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTVEFLEENS FSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYY SGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVR DSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKC YKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFR FPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEI PETVRTVQLIKDLAREIRLVEDIFQQN
>3KV4_2 Histone H3-like (chains B) ARTKQTARKSTGGKAPRKQLATKA
Water and common crystallization additives (EDO) are not listed.
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Horton, J.R., Upadhyay, A.K., Qi, H.H. et al. Nat Struct Mol Biol (2010) 17:38-43. DOI 10.1038/nsmb.1753 · PubMed
Other PDB entries of the same protein (UniProt Q9UPP1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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