Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11. Determined by X-ray diffraction at 2.65 Å resolution. Released 20 Jan 2016.
Explore 5C46 in 3D Show helices and sheets RCSB PDB PDBe
5C46 contains 36 α-helices and 17 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 |
|---|---|---|---|
| α-helix | 129-134 | 6 | |
| α-helix | 141-150 | 10 | |
| α-helix | 154-163 | 10 | |
| α-helix | 164-166 | 3 | |
| α-helix | 169-173 | 5 | |
| α-helix | 176-185 | 10 | |
| α-helix | 188-204 | 17 | |
| α-helix | 206-218 | 13 | |
| α-helix | 234-242 | 9 | |
| α-helix | 308-323 | 16 | |
| α-helix | 324-326 | 3 | |
| α-helix | 330-341 | 12 | |
| α-helix | 345-347 | 3 | |
| β-strand | 361-365 | 5 | 1 |
| α-helix | 368-370 | 3 | |
| β-strand | 372-373 | 2 | 1 |
| β-strand | 382-390 | 9 | 1 |
| α-helix | 399-402 | 4 | |
| α-helix | 522-531 | 10 | |
| β-strand | 541-549 | 9 | 1 |
| α-helix | 555-573 | 19 | |
| β-strand | 585-587 | 3 | 1 |
| β-strand | 593-595 | 3 | 1 |
| α-helix | 597-598 | 2 | |
| β-strand | 601-603 | 3 | 2 |
| α-helix | 604-610 | 7 | |
| α-helix | 615-622 | 8 | |
| α-helix | 629-652 | 24 | |
| β-strand | 662-665 | 4 | 2 |
| β-strand | 670-672 | 3 | 2 |
| α-helix | 697-702 | 6 | |
| α-helix | 709-726 | 18 | |
| α-helix | 729-740 | 12 | |
| α-helix | 746-748 | 3 | |
| α-helix | 753-759 | 7 | |
| α-helix | 767-781 | 15 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10-18 | 9 | 3 |
| α-helix | 24-32 | 9 | |
| α-helix | 40-43 | 4 | |
| β-strand | 46-55 | 10 | 3 |
| β-strand | 58-67 | 10 | 3 |
| α-helix | 71-73 | 3 | |
| α-helix | 74-77 | 4 | |
| β-strand | 86-92 | 7 | 3 |
| α-helix | 96-100 | 5 | |
| α-helix | 102-112 | 11 | |
| β-strand | 118-124 | 7 | 3 |
| α-helix | 129-131 | 3 | |
| α-helix | 136-145 | 10 | |
| β-strand | 149-152 | 4 | 3 |
| β-strand | 154 | 1 | 4 |
| β-strand | 159 | 1 | 4 |
| α-helix | 161-178 | 18 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Phosphatidylinositol 4-kinase beta | E | protein | 529 | Homo sapiens | Q9UBF8 (AlphaFold model) |
| Ras-related protein Rab-11A | F | protein | 219 | Homo sapiens | P62491 (AlphaFold model) |
>5C46_1 Phosphatidylinositol 4-kinase beta (chains E) GSHMQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYL PQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKL RKLILSDELKPANLKRTAANPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQ RLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFD TTSVPARIPENRRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLR QELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSL LDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDF GFILSSSPRNLGFETSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQI VEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS
>5C46_2 Ras-related protein Rab-11A (chains F) GSHMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDG KTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI VIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS QKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQCCQNI
| ID | Name | Formula | Copies |
|---|---|---|---|
| GSP | 5'-guanosine-diphosphate-monothiophosphate | C10 H16 N5 O13 P3 S | 1 |
| MG | Magnesium ion | Mg | 1 |
Water and common crystallization additives (SO4) are not listed.
Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11. Fowler, M.L., McPhail, J.A., Jenkins, M.L. et al. Protein Sci (2016) 25:826-839. DOI 10.1002/pro.2879 · PubMed
Other PDB entries of the same protein (UniProt Q9UBF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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