8ZLK: PWWP domain from human DNMT3B

PWWP domain from human DNMT3B. Determined by X-ray diffraction at 2.74 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 2.74 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,170
Mol. weight: 33.51 kDa
Released: 2 Apr 2025

Explore 8ZLK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZLK contains 15 α-helices and 10 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.

Chain A: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	1
β-strand	239-244	6	1
α-helix	246-249	4
α-helix	253-255	3
β-strand	258-263	6	1
β-strand	269-273	5	1
α-helix	274-276	3
β-strand	277-279	3	1
α-helix	283-286	4
α-helix	289-294	6
α-helix	296-313	18
α-helix	325-337	13
α-helix	345-348	4

Chain B: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	2
β-strand	239-244	6	2
α-helix	246-249	4
α-helix	253-255	3
β-strand	258-263	6	2
β-strand	269-273	5	2
α-helix	274-276	3
β-strand	277-279	3	2
α-helix	289-294	6
α-helix	296-312	17
α-helix	325-336	12
α-helix	345-348	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3B	A, B	protein	151	Homo sapiens	Q9UBC3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8ZLK_1 DNA (cytosine-5)-methyltransferase 3B (chains A, B)
GEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWF
GDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDS
LEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

Primary citation

Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation. Cho, C.C., Huang, H.H., Jiang, B.C. et al. Sci Adv (2025) 11:eadu8116-eadu8116. DOI 10.1126/sciadv.adu8116 · PubMed

Other PDB entries of the same protein (UniProt Q9UBC3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NRR 1.7 Å, Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol
3FLG 1.8 Å, The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta
5NV2 2.03 Å, Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S)
3QKJ 2.04 Å, The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a…
5NRV 2.08 Å, Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol
7O45 2.1 Å, Crystal structure of ADD domain of the human DNMT3B methyltransferase
5CIU 2.24 Å, Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
6R3E 2.27 Å, Human DNMT3B PWWP domain in complex with triisopropanolamine
5NR3 2.3 Å, Human DNMT3B PWWP domain in complex with ethambutol
5NRS 2.3 Å, Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine
5NV0 2.4 Å, Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile
5NVO 2.4 Å, Human DNMT3B PWWP domain in complex with choline

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