crystal structure of KRYPTONITE in complex with mCHG DNA and SAH. Determined by X-ray diffraction at 3.1 Å resolution. Released 30 Jul 2014.
Explore 4QEP in 3D Show helices and sheets RCSB PDB PDBe
4QEP contains 13 α-helices and 37 β-strands across 1 chain. 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 | 101-121 | 21 | |
| α-helix | 127-137 | 11 | |
| β-strand | 151 | 1 | 1 |
| β-strand | 154 | 1 | 1 |
| β-strand | 159-160 | 2 | 2 |
| α-helix | 163-169 | 7 | |
| β-strand | 179-182 | 4 | 2 |
| α-helix | 184-186 | 3 | |
| β-strand | 197-203 | 7 | 2 |
| β-strand | 211-212 | 2 | 2 |
| β-strand | 216-220 | 5 | 2 |
| α-helix | 242-252 | 11 | |
| β-strand | 256-263 | 8 | 2 |
| β-strand | 271-288 | 18 | 2 |
| β-strand | 294-302 | 9 | 2 |
| β-strand | 331-333 | 3 | 3 |
| β-strand | 347-348 | 2 | 3 |
| β-strand | 363-364 | 2 | 4 |
| β-strand | 369-370 | 2 | 5 |
| α-helix | 377-378 | 2 | |
| β-strand | 379 | 1 | 6 |
| α-helix | 380 | 1 | |
| β-strand | 387 | 1 | 7 |
| α-helix | 396-400 | 5 | |
| β-strand | 407-408 | 2 | 8 |
| β-strand | 414-415 | 2 | 8 |
| β-strand | 421-423 | 3 | 9 |
| β-strand | 431 | 1 | 7 |
| α-helix | 436-441 | 6 | |
| β-strand | 448-452 | 5 | 3 |
| β-strand | 458-462 | 5 | 3 |
| β-strand | 466 | 1 | 10 |
| β-strand | 471-474 | 4 | 9 |
| β-strand | 478-481 | 4 | 5 |
| α-helix | 482-484 | 3 | |
| β-strand | 494-496 | 3 | 5 |
| β-strand | 536-539 | 4 | 5 |
| β-strand | 543-544 | 2 | 4 |
| α-helix | 546-549 | 4 | |
| β-strand | 551-552 | 2 | 11 |
| β-strand | 558-564 | 7 | 9 |
| β-strand | 567 | 1 | 6 |
| α-helix | 570-572 | 3 | |
| β-strand | 574-579 | 6 | 9 |
| β-strand | 583 | 1 | 10 |
| β-strand | 588 | 1 | 3 |
| β-strand | 590-591 | 2 | 11 |
| α-helix | 595-596 | 2 | |
| β-strand | 611 | 1 | 12 |
| β-strand | 622 | 1 | 12 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | A | protein | 533 | Arabidopsis thaliana | Q8GZB6 (AlphaFold model) |
| DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3') | C | DNA | 15 | ||
| DNA (5'-d(*ap*cp*tp*gp*cp*tp*gp*ap*gp*tp*ap*cp*cp*ap*t)-3') | D | DNA | 15 |
>4QEP_1 Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (chains A) SNGKDVNLEPHLKVTKCLRLFNKQYLLCVQAKLSRPDLKGVTEMIKAKAILYPRKIIGDL PGIDVGHRFFSRAEMCAVGFHNHWLNGIDYMSMEYEKEYSNYKLPLAVSIVMSGQYEDDL DNADTVTYTGQGGHNLTGNKRQIKDQLLERGNLALKHCCEYNVPVRVTRGHNCKSSYTKR VYTYDGLYKVEKFWAQKGVSGFTVYKYRLKRLEGQPELTTDQVNFVAGRIPTSTSEIEGL VCEDISGGLEFKGIPATNRVDDSPVSPTSGFTYIKSLIIEPNVIIPKSSTGCNCRGSCTD SKKCACAKLNGGNFPYVDLNDGRLIESRDVVFECGPHCGCGPKCVNRTSQKRLRFNLEVF RSAKKGWAVRSWEYIPAGSPVCEYIGVVRRTADVDTISDNEYIFEIDCQQTMQGLGGRQR RLRDVAVPMNNGVSQSSEDENAPEFCIDAGSTGNFARFINHSCEPNLFVQCVLSSHQDIR LARVVLFAADNISPMQELTYDYGYALDSVHGPDGKVKQLACYCGALNCRKRLY
>4QEP_2 DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3') (chains C) GGTACTCAGCAGTAT
>4QEP_3 DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3') (chains D) ACTGCTGAGTACCAT
Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE. Du, J., Johnson, L.M., Groth, M. et al. Mol Cell (2014) 55:495-504. DOI 10.1016/j.molcel.2014.06.009 · PubMed
Other PDB entries of the same protein (UniProt Q8GZB6 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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