5CIU: DNA-methyltransferase 3B

Name: PDB 5CIU: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
Published: 2016-03-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain. Determined by X-ray diffraction at 2.24 Å resolution. Released 30 Mar 2016.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,266
Mol. weight: 36.83 kDa
Released: 30 Mar 2016

Explore 5CIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CIU contains 15 α-helices and 12 β-strands across 4 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	1
β-strand	239-244	6	1
α-helix	246-248	3
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	289-294	6
α-helix	296-313	18
α-helix	329-337	9
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	246-248	3
α-helix	253-255	3
β-strand	258-263	6	2
β-strand	269-273	5	2
α-helix	274-276	3
β-strand	278-279	2	2
α-helix	283-286	4
α-helix	296-313	18
α-helix	330-337	8
α-helix	345-347	3

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	35	1	2

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	35	1	1
α-helix	36-37	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3B	A, B	protein	150	Homo sapiens	Q9UBC3 (AlphaFold model)
Histone H3.2	C, D	protein	15	Homo sapiens	Q71DI3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5CIU_1 DNA (cytosine-5)-methyltransferase 3B (chains A, B)
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFG
DGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSL
EDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

Sequence of entity 2 (C, D), FASTA

>5CIU_2 Histone H3.2 (chains C, D)
SAPATGGVKKPHRYR

Primary citation

Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B. Rondelet, G., Dal Maso, T., Willems, L. et al. J Struct Biol (2016) 194:357-367. DOI 10.1016/j.jsb.2016.03.013 · 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
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
5NV7 2.57 Å, Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine

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