8TE4: DNA-methyltransferase 3A

Name: PDB 8TE4: Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer
Published: 2024-03-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer. Determined by X-ray diffraction at 2.65 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,869
Mol. weight: 265.39 kDa
Ligands: SAH
Released: 13 Mar 2024

Explore 8TE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TE4 contains 112 α-helices and 100 β-strands across 8 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: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	634-639	6	1
α-helix	645-652	8
β-strand	655	1	2
β-strand	657-663	7	1
α-helix	667-676	10
β-strand	682-683	2	1
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	1
β-strand	714	1	3
α-helix	730-741	12
α-helix	743-744	2
β-strand	752-758	7	1
β-strand	761	1	3
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-781	4	1
α-helix	782-784	3
β-strand	788	1	4
β-strand	791-796	6	1
α-helix	804-806	3
α-helix	815-818	4
α-helix	820	1
β-strand	823-825	3	5
β-strand	830	1	4
β-strand	850-852	3	5
β-strand	855-857	3	5
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-890	9
α-helix	893-894	2
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	2

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	634-639	6	6
α-helix	645-652	8
β-strand	655	1	7
β-strand	657-663	7	6
α-helix	667-676	10
β-strand	682-683	2	6
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	6
β-strand	714	1	8
α-helix	730-741	12
α-helix	743-744	2
β-strand	752-758	7	6
β-strand	761	1	8
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-781	4	6
α-helix	782-784	3
β-strand	788	1	9
β-strand	791-796	6	6
α-helix	804-806	3
α-helix	815-818	4
α-helix	820	1
β-strand	823-825	3	10
β-strand	830	1	9
β-strand	850-852	3	10
β-strand	855-857	3	10
α-helix	858-860	3
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-891	10
α-helix	893-894	2
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	7

Chain C: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	634-639	6	11
α-helix	645-652	8
β-strand	655	1	12
β-strand	657-663	7	11
α-helix	667-676	10
β-strand	682-683	2	11
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	11
β-strand	714	1	13
α-helix	730-741	12
α-helix	743-744	2
β-strand	752-758	7	11
β-strand	761	1	13
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-781	4	11
α-helix	782-784	3
β-strand	788-789	2	14
β-strand	791-796	6	11
α-helix	804-806	3
α-helix	815-818	4
α-helix	820	1
β-strand	823-825	3	15
β-strand	830-831	2	14
β-strand	850-852	3	15
β-strand	855-857	3	15
α-helix	858-860	3
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-890	9
α-helix	893-894	2
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	12

Chain D: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	634-639	6	22
α-helix	645-652	8
β-strand	655	1	23
β-strand	657-663	7	22
α-helix	667-676	10
β-strand	682-683	2	22
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	22
β-strand	714	1	24
α-helix	730-741	12
α-helix	743-744	2
β-strand	752-758	7	22
β-strand	761	1	24
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-781	4	22
α-helix	782-784	3
β-strand	788	1	25
β-strand	791-796	6	22
α-helix	804-806	3
α-helix	815-818	4
α-helix	820	1
β-strand	823-825	3	26
β-strand	830	1	25
β-strand	850-852	3	26
β-strand	855-857	3	26
α-helix	858-860	3
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-890	9
α-helix	893-894	2
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	23

Chain E: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	634-638	5	16
α-helix	645-652	8
β-strand	655	1	17
β-strand	657-664	8	16
β-strand	681-686	6	16
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-707	5	16
α-helix	730-741	12
α-helix	743-744	2
β-strand	752-758	7	16
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-779	2	16
β-strand	792-796	5	16
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	17

Chain F: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	634-640	7	20
α-helix	645-652	8
β-strand	655	1	21
β-strand	657-664	8	20
β-strand	681-686	6	20
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-707	5	20
α-helix	728-741	14
α-helix	743-744	2
β-strand	752-758	7	20
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-779	2	20
β-strand	792-796	5	20
α-helix	896-902	7
α-helix	903-907	5
β-strand	911	1	21

Chain G: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	634-638	5	27
α-helix	645-652	8
β-strand	655	1	28
β-strand	657-664	8	27
β-strand	681-686	6	27
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-707	5	27
α-helix	728-741	14
α-helix	743-744	2
β-strand	752-758	7	27
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-779	2	27
β-strand	792-796	5	27
α-helix	892-894	3
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	28

Chain H: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	634-640	7	18
α-helix	645-652	8
β-strand	655	1	19
β-strand	657-664	8	18
β-strand	681-686	6	18
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-707	5	18
α-helix	728-741	14
α-helix	743-744	2
β-strand	752-758	7	18
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-780	3	18
β-strand	792-796	5	18
α-helix	896-902	7
α-helix	903-907	5
β-strand	911	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A	A, B, C, D, E, F, G, H	protein	287	Homo sapiens	Q9Y6K1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>8TE4_1 DNA (cytosine-5)-methyltransferase 3A (chains A, B, C, D, E, F, G, H)
GSAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVG
DVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKE
GDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPL
ASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEME
RVFGFPVHYTDVSAMSHLARQRLLGRSWSVPVIRHLFAPLKEYFACV

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4

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

Primary citation

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Lu, J., Guo, Y., Yin, J. et al. Nat Commun (2024) 15:3111-3111. DOI 10.1038/s41467-024-47398-y · PubMed

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
4QBQ 2.41 Å, Crystal structure of DNMT3a ADD domain bound to H3 peptide
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

Browse structure collections

About this viewer

MolViewer shows 8TE4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.