4QBQ: DNMT3a ADD domain

Name: PDB 4QBQ: Crystal structure of DNMT3a ADD domain bound to H3 peptide
Published: 2015-05-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of DNMT3a ADD domain bound to H3 peptide. Determined by X-ray diffraction at 2.41 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,299
Mol. weight: 32.1 kDa
Ligands: ZN
Released: 13 May 2015

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

Secondary structure: helices and β-sheets

4QBQ contains 13 α-helices and 25 β-strands across 3 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: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	475-484	10
α-helix	490-492	3
β-strand	494	1	1
β-strand	504-505	2	1
β-strand	509	1	2
β-strand	512-513	2	1
α-helix	515-524	10
β-strand	528	1	3
β-strand	534	1	3
β-strand	537	1	4
β-strand	546-548	3	4
β-strand	557-559	3	4
α-helix	560-566	7
α-helix	571-576	6
β-strand	591-592	2	5
β-strand	595-596	2	5
β-strand	597	1	2
α-helix	601-608	8

Chain C: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	476-484	9
α-helix	490-492	3
β-strand	494	1	6
β-strand	504-505	2	6
β-strand	509	1	7
β-strand	512-513	2	6
α-helix	515-523	9
β-strand	528	1	8
β-strand	534	1	8
β-strand	537	1	9
β-strand	545-548	4	9
β-strand	557-559	3	9
α-helix	560-562	3
α-helix	563-567	5
α-helix	571-577	7
β-strand	591-592	2	10
β-strand	595-596	2	10
β-strand	597	1	7
α-helix	601-608	8

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-5	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A	A, C	protein	137	Homo sapiens	Q9Y6K1 (AlphaFold model)
Histone H3	P	protein	8	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4QBQ_1 DNA (cytosine-5)-methyltransferase 3A (chains A, C)
GPLGSLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGY
QSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYG
LLRRREDWPSRLQMFFA

Sequence of entity 2 (P), FASTA

>4QBQ_2 Histone H3 (chains P)
ARTKQTAR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs. Noh, K., Wang, H., Kim, H. et al. To be published.

Other PDB entries of the same protein (UniProt Q9Y6K1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8BA5 1.45 Å, Crystal structure of the DNMT3A ADD domain
4QBS 1.8 Å, Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide
4QBR 1.9 Å, Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide
3A1B 2.29 Å, Crystal structure of the DNMT3A ADD domain in complex with histone H3
3A1A 2.3 Å, Crystal Structure of the DNMT3A ADD domain
3LLR 2.3 Å, Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha
3SVM 2.31 Å, Human MPP8 - human DNMT3AK47me2 peptide
6W8B 2.4 Å, Structure of DNMT3A in complex with CGA DNA
6W8J 2.44 Å, Structure of DNMT3A (R882H) in complex with CAG DNA
8TE1 2.48 Å, Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer
6W89 2.5 Å, Structure of DNMT3A (R882H) in complex with CGA DNA
6W8D 2.6 Å, Structure of DNMT3A (R882H) in complex with CGT DNA

Browse structure collections

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