3A1B: DNMT3A ADD domain

Name: PDB 3A1B: Crystal structure of the DNMT3A ADD domain in complex with histone H3
Published: 2009-11-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of the DNMT3A ADD domain in complex with histone H3. Determined by X-ray diffraction at 2.29 Å resolution. Released 10 Nov 2009.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,250
Mol. weight: 18.7 kDa
Ligands: ZN
Released: 10 Nov 2009

Explore 3A1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3A1B contains 9 α-helices and 12 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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	457-460	4	1
α-helix	461-463	3
α-helix	473-484	12
α-helix	490-492	3
β-strand	494	1	2
β-strand	504-505	2	2
β-strand	509	1	3
β-strand	512-513	2	2
α-helix	515-524	10
β-strand	528	1	4
β-strand	534	1	4
β-strand	545-548	4	1
α-helix	549	1
β-strand	557-559	3	1
α-helix	560-562	3
α-helix	563-567	5
α-helix	571-576	6
β-strand	591-592	2	5
β-strand	595-596	2	5
β-strand	597	1	3
α-helix	601-609	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A, Histone H3.1	A	protein	159	Homo sapiens	P68431 (AlphaFold model), Q9Y6K1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3A1B_1 DNA (cytosine-5)-methyltransferase 3A, Histone H3.1 (chains A)
ARTKQTARKSTGGKAPRKQLRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQ
NCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAA
IKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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

Primary citation

Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. Otani, J., Nankumo, T., Arita, K. et al. EMBO Rep (2009) 10:1235-1241. DOI 10.1038/embor.2009.218 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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