7O45: ADD domain of the human DNMT3B methyltransferase

Name: PDB 7O45: Crystal structure of ADD domain of the human DNMT3B methyltransferase
Published: 2022-04-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of ADD domain of the human DNMT3B methyltransferase. Determined by X-ray diffraction at 2.1 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,065
Mol. weight: 67.25 kDa
Ligands: ZN
Released: 13 Apr 2022

Explore 7O45 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O45 contains 28 α-helices and 48 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: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	417-425	9
α-helix	431-433	3
β-strand	434	1	1
β-strand	435	1	2
β-strand	441	1	1
β-strand	445-446	2	2
β-strand	450	1	3
β-strand	453-454	2	2
α-helix	456-463	8
β-strand	469	1	4
β-strand	475	1	4
β-strand	478	1	5
β-strand	487-489	3	5
β-strand	498-500	3	5
α-helix	501-503	3
α-helix	504-508	5
α-helix	512-517	6
α-helix	522-524	3
β-strand	532-533	2	6
β-strand	536-537	2	6
β-strand	538	1	3
α-helix	542-551	10

Chains B and C: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	417-425	9
α-helix	431-433	3
β-strand	434	1	7
β-strand	435	1	8
β-strand	441	1	7
β-strand	445-446	2	8
β-strand	450	1	9
β-strand	453-454	2	8
α-helix	456-463	8
β-strand	469	1	10
β-strand	475	1	10
β-strand	478	1	11
β-strand	487-489	3	11
β-strand	498-500	3	11
α-helix	501-503	3
α-helix	504-508	5
α-helix	512-518	7
α-helix	522-523	2
β-strand	532-533	2	12
β-strand	536-537	2	12
β-strand	538	1	9
α-helix	542-551	10

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	421-425	5
β-strand	435	1	19
β-strand	450	1	20
β-strand	453	1	19
α-helix	487-489	3
α-helix	501-507	7
β-strand	532-533	2	21
β-strand	536-537	2	21
β-strand	538	1	20
α-helix	542-549	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 6 of DNA (cytosine-5)-methyltransferase 3B	A, B, C, D	protein	146	Homo sapiens	Q9UBC3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7O45_1 Isoform 6 of DNA (cytosine-5)-methyltransferase 3B (chains A, B, C, D)
SGSDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYM
YDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCL
PQRCHGVLRRRKDWNVRLQAFFTSDT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Water and common crystallization additives (BR) are not listed.

Primary citation

Structure of the DNMT3B ADD domain suggests the absence of a DNMT3A-like autoinhibitory mechanism. Boyko, K., Arkova, O., Nikolaeva, A. et al. Biochem Biophys Res Commun (2022) 619:124-129. DOI 10.1016/j.bbrc.2022.06.036 · 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
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
5NV7 2.57 Å, Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine

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