Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 10 Apr 2019.
Explore 6IP4 in 3D Show helices and sheets RCSB PDB PDBe
6IP4 contains 24 α-helices and 24 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 | 95-99 | 5 | |
| α-helix | 100-101 | 2 | |
| β-strand | 102 | 1 | 1 |
| α-helix | 103-104 | 2 | |
| β-strand | 105-106 | 2 | 2 |
| α-helix | 110-113 | 4 | |
| α-helix | 116-127 | 12 | |
| α-helix | 128-130 | 3 | |
| β-strand | 132-136 | 5 | 2 |
| α-helix | 145-147 | 3 | |
| α-helix | 148-152 | 5 | |
| β-strand | 157-159 | 3 | 3 |
| β-strand | 161-164 | 4 | 4 |
| α-helix | 172-179 | 8 | |
| β-strand | 184-186 | 3 | 3 |
| α-helix | 187-202 | 16 | |
| α-helix | 210-223 | 14 | |
| β-strand | 228-231 | 4 | 4 |
| β-strand | 232-235 | 4 | 2 |
| α-helix | 255-258 | 4 | |
| α-helix | 265-268 | 4 | |
| β-strand | 274 | 1 | 5 |
| β-strand | 278 | 1 | 5 |
| β-strand | 280-284 | 5 | 2 |
| β-strand | 289-293 | 5 | 1 |
| β-strand | 300-308 | 9 | 2 |
| β-strand | 311-315 | 5 | 1 |
| α-helix | 318-320 | 3 | |
| α-helix | 321-333 | 13 | |
| α-helix | 347-351 | 5 | |
| α-helix | 355-356 | 2 | |
| α-helix | 359-364 | 6 | |
| β-strand | 370-374 | 5 | 1 |
| β-strand | 378-382 | 5 | 2 |
| β-strand | 388-392 | 5 | 1 |
| β-strand | 396-403 | 8 | 2 |
| α-helix | 406-408 | 3 | |
| α-helix | 409-421 | 13 | |
| α-helix | 430-441 | 12 | |
| α-helix | 454-484 | 31 | |
| β-strand | 487-493 | 7 | 6 |
| β-strand | 498-499 | 2 | 7 |
| β-strand | 506-507 | 2 | 7 |
| β-strand | 510-513 | 4 | 6 |
| β-strand | 521 | 1 | 6 |
| α-helix | 527-529 | 3 | |
| β-strand | 538-543 | 6 | 6 |
| α-helix | 546-558 | 13 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Arabidopsis JMJ13 | A | protein | 490 | Arabidopsis thaliana | F4KIX0 (AlphaFold model) |
| Histone H3.2 | B | protein | 12 | Arabidopsis thaliana | P59226 (AlphaFold model) |
>6IP4_1 Arabidopsis JMJ13 (chains A) SETDDLKWTERLPECPVYRPTKEEFEDPLTYLQKIFPEASKYGICKIVSPLTATVPAGAV LMKEKSNFKFTTRVQPLRLAEWDSDDKVTFFMSGRTYTFRDYEKMANKVFARRYCSGGSL PDSFLEKEFWKEIACGKTETVEYACDVDGSAFSSAPGDPLGSSKWNLNKVSRLPKSTLRL LETSIPGVTEPMLYIGMLFSMFAWHVEDHYLYSINYQHCGASKTWYGIPGSAALKFEKVV KECVYNDDILSTNGEDGAFDVLLGKTTIFPPKTLLDHNVPVYKAVQKPGEFVVTFPRAYH AGFSHGFNCGEAVNFAMGDWFPFGAIASCRYAHLNRVPLLPHEELICKEAMLLNSSSKSE NLDLTPTELSGQRSIKTAFVHLIRFLHLARWSLMKSGLCTGLVSNTYGTIVCSLCKRDCY LAFINCECYSHPVCLRHDVKKLDLPCGTTHTLYLRDNIEDMEAAAMKFEKEDGVSDLITT DEDLYKYPSS
>6IP4_2 Histone H3.2 (chains B) AARKSAPATGGV
Water and common crystallization additives (SO4) are not listed.
The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor. Zheng, S., Hu, H., Ren, H. et al. Nat Commun (2019) 10:1303-1303. DOI 10.1038/s41467-019-09310-x · PubMed
Other PDB entries of the same protein (UniProt F4KIX0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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