4QEO: KRYPTONITE

crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH. Determined by X-ray diffraction at 2.0 Å resolution. Released 30 Jul 2014.

Method
X-ray diffraction
Resolution
2.0 Å
Organisms
Arabidopsis thaliana, Synthetic construct, Xenopus laevis
Chains
4
Atoms
4,570
Mol. weight
71.09 kDa
Ligands
ZN, SAH
Released
30 Jul 2014

Explore 4QEO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QEO contains 25 α-helices and 39 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.

Chain A: 25 helices, 39 β-strands

ElementResiduesLengthSheet
α-helix101-12121
α-helix127-13711
α-helix150-1512
α-helix1581
β-strand159-16021
α-helix163-1697
β-strand179-18241
α-helix184-1863
α-helix1941
α-helix1961
β-strand197-20371
β-strand211-21331
β-strand216-22051
α-helix2211
β-strand22512
β-strand23312
α-helix242-25211
β-strand256-26381
β-strand271-288181
β-strand294-30291
α-helix3031
α-helix307-3115
β-strand331-33333
β-strand347-34823
β-strand363-36424
β-strand369-37025
α-helix377-3782
β-strand37916
α-helix3801
β-strand38717
α-helix396-4005
β-strand407-40828
β-strand414-41528
β-strand422-42329
β-strand43117
α-helix436-4416
α-helix443-4442
β-strand448-45253
β-strand458-46253
β-strand466110
β-strand471-47449
β-strand478-48145
α-helix482-4843
β-strand494-49635
β-strand536-53945
β-strand543-54424
α-helix546-5494
α-helix5501
β-strand551-552211
β-strand558-56479
β-strand56716
α-helix570-5723
β-strand574-57969
β-strand583110
α-helix5871
β-strand58813
α-helix5891
β-strand590-591211
α-helix595-5962
β-strand600-601212
α-helix6061
β-strand607-608212
β-strand611113
β-strand622113

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4Aprotein533Arabidopsis thalianaQ8GZB6 (AlphaFold model)
DNA 5'-GGTACT(5CM)ATCAGTAT-3'CDNA15Synthetic construct
DNA 5'-actgatgagtaccat-3'DDNA15Synthetic construct
Histone H3Pprotein15Xenopus laevisP84233 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>4QEO_1 Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (chains A)
SNGKDVNLEPHLKVTKCLRLFNKQYLLCVQAKLSRPDLKGVTEMIKAKAILYPRKIIGDL
PGIDVGHRFFSRAEMCAVGFHNHWLNGIDYMSMEYEKEYSNYKLPLAVSIVMSGQYEDDL
DNADTVTYTGQGGHNLTGNKRQIKDQLLERGNLALKHCCEYNVPVRVTRGHNCKSSYTKR
VYTYDGLYKVEKFWAQKGVSGFTVYKYRLKRLEGQPELTTDQVNFVAGRIPTSTSEIEGL
VCEDISGGLEFKGIPATNRVDDSPVSPTSGFTYIKSLIIEPNVIIPKSSTGCNCRGSCTD
SKKCACAKLNGGNFPYVDLNDGRLIESRDVVFECGPHCGCGPKCVNRTSQKRLRFNLEVF
RSAKKGWAVRSWEYIPAGSPVCEYIGVVRRTADVDTISDNEYIFEIDCQQTMQGLGGRQR
RLRDVAVPMNNGVSQSSEDENAPEFCIDAGSTGNFARFINHSCEPNLFVQCVLSSHQDIR
LARVVLFAADNISPMQELTYDYGYALDSVHGPDGKVKQLACYCGALNCRKRLY
Sequence of entity 2 (C), FASTA
>4QEO_2 DNA 5'-GGTACT(5CM)ATCAGTAT-3' (chains C)
GGTACTCATCAGTAT
Sequence of entity 3 (D), FASTA
>4QEO_3 DNA 5'-ACTGATGAGTACCAT-3' (chains D)
ACTGATGAGTACCAT
Sequence of entity 4 (P), FASTA
>4QEO_4 Histone H3 (chains P)
ARTKQTARKSTGGKA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4
SAHS-adenosyl-L-homocysteineC14 H20 N6 O5 S1

Primary citation

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:

Browse structure collections

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