6Q2V: SPOC domain of human PHD-finger protein 3
Crystal structure of SPOC domain of human PHD-finger protein 3 (PHF3). Determined by X-ray diffraction at 2.59 Å resolution. Released 15 Jul 2020.
- Method
- X-ray diffraction
- Resolution
- 2.59 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 9,414
- Mol. weight
- 147.37 kDa
- Released
- 15 Jul 2020
Explore 6Q2V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Q2V contains 44 α-helices and 62 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.
Chains A and D: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 1 |
| β-strand | 1219-1229 | 11 | 1 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1249 | 8 | 1 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 1 |
| α-helix | 1279-1295 | 17 | |
| β-strand | 1298-1301 | 4 | 1 |
| β-strand | 1308-1316 | 9 | 1 |
| α-helix | 1321-1323 | 3 | |
| α-helix | 1324-1326 | 3 | |
| β-strand | 1341-1349 | 9 | 1 |
| β-strand | 1352 | 1 | 2 |
Chain B: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 3 |
| β-strand | 1219-1229 | 11 | 3 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1249 | 8 | 3 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 3 |
| α-helix | 1279-1294 | 16 | |
| β-strand | 1298-1301 | 4 | 3 |
| β-strand | 1310-1316 | 7 | 3 |
| α-helix | 1320-1323 | 4 | |
| α-helix | 1324-1326 | 3 | |
| β-strand | 1341-1349 | 9 | 3 |
Chain C: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1214 | 6 | 4 |
| β-strand | 1220-1229 | 10 | 4 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1249 | 8 | 4 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 4 |
| α-helix | 1279-1293 | 15 | |
| β-strand | 1298-1301 | 4 | 4 |
| β-strand | 1308-1316 | 9 | 4 |
| α-helix | 1321-1323 | 3 | |
| α-helix | 1324-1326 | 3 | |
| α-helix | 1327 | 1 | |
| α-helix | 1329 | 1 | |
| β-strand | 1341-1349 | 9 | 4 |
| β-strand | 1352 | 1 | 5 |
Chain E: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 7 |
| β-strand | 1219-1229 | 11 | 7 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1249 | 8 | 7 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 7 |
| α-helix | 1282-1295 | 14 | |
| β-strand | 1298-1301 | 4 | 7 |
| β-strand | 1308-1316 | 9 | 7 |
| α-helix | 1320-1323 | 4 | |
| α-helix | 1327 | 1 | |
| α-helix | 1329 | 1 | |
| β-strand | 1341-1349 | 9 | 7 |
Chain F: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 8 |
| β-strand | 1219-1229 | 11 | 8 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1247 | 6 | 8 |
| β-strand | 1248 | 1 | 2 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 8 |
| α-helix | 1279-1295 | 17 | |
| β-strand | 1299-1301 | 3 | 8 |
| β-strand | 1308-1316 | 9 | 8 |
| α-helix | 1320-1323 | 4 | |
| α-helix | 1324-1326 | 3 | |
| β-strand | 1341-1349 | 9 | 8 |
Chain G: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 5 |
| β-strand | 1219-1229 | 11 | 5 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1249 | 8 | 5 |
| α-helix | 1251-1264 | 14 | |
| β-strand | 1269-1276 | 8 | 5 |
| α-helix | 1280-1294 | 15 | |
| β-strand | 1298-1301 | 4 | 5 |
| β-strand | 1310-1316 | 7 | 5 |
| α-helix | 1321-1323 | 3 | |
| α-helix | 1327 | 1 | |
| α-helix | 1329 | 1 | |
| β-strand | 1341-1347 | 7 | 5 |
Chain H: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1209-1215 | 7 | 9 |
| β-strand | 1219-1229 | 11 | 9 |
| α-helix | 1235-1238 | 4 | |
| β-strand | 1242-1244 | 3 | 9 |
| β-strand | 1245 | 1 | 10 |
| α-helix | 1251-1263 | 13 | |
| β-strand | 1267-1276 | 10 | 9 |
| α-helix | 1279-1295 | 17 | |
| β-strand | 1299-1300 | 2 | 9 |
| β-strand | 1301 | 1 | 10 |
| β-strand | 1308-1316 | 9 | 9 |
| α-helix | 1320-1323 | 4 | |
| α-helix | 1324-1326 | 3 | |
| β-strand | 1341-1349 | 9 | 9 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| PHD finger protein 3 | A, B, C, D, E, F, G, H | protein | 162 | Homo sapiens | Q92576 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>6Q2V_1 PHD finger protein 3 (chains A, B, C, D, E, F, G, H)
GAMGSTFLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTV
WDYVEKIKASGTKEICVVRFTPVTEEDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLI
PLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIRQKLKRQHS
Primary citation
PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Appel, L.M., Franke, V., Bruno, M. et al. Nat Commun (2021) 12:6078. DOI 10.1038/s41467-021-26360-2
Other PDB entries of the same protein (UniProt Q92576 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6IC9 1.75 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
- 6IC8 1.93 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
- 6Q5Y 2.85 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
- 2DME Solution structure of the TFIIS domain II of human PHD finger protein 3
Browse structure collections
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