5YX2: DNMT3A-DNMT3L

Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites. Determined by X-ray diffraction at 2.65 Å resolution. Released 31 Jan 2018.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 8,380
Mol. weight: 130.25 kDa
Ligands: SAH
Released: 31 Jan 2018

Explore 5YX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YX2 contains 59 α-helices and 46 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: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	634-639	6	1
α-helix	645-652	8
β-strand	657-663	7	1
α-helix	667-676	10
β-strand	681-683	3	1
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	1
β-strand	714	1	2
α-helix	728-730	3
α-helix	731-741	11
α-helix	743-744	2
β-strand	752-758	7	1
β-strand	761	1	2
α-helix	763-773	11
β-strand	778-781	4	1
α-helix	782-784	3
β-strand	788	1	3
β-strand	791-796	6	1
α-helix	804-808	5
α-helix	815-818	4
β-strand	824-825	2	4
β-strand	830	1	3
α-helix	837-840	4
β-strand	842	1	5
β-strand	847	1	5
β-strand	850-852	3	4
β-strand	855-857	3	4
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-891	10
α-helix	895-902	8
α-helix	903-905	3

Chain B: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	184-186	3
α-helix	189-191	3
β-strand	192-195	4	6
α-helix	200-206	7
β-strand	218-221	4	6
α-helix	229-234	6
β-strand	240-244	5	6
α-helix	245-247	3
α-helix	256-269	14
α-helix	271-273	3
β-strand	281-286	6	6
α-helix	292-301	10
β-strand	307-311	5	6
β-strand	319-325	7	6
α-helix	328-332	5
α-helix	335-337	3
α-helix	340-352	13
α-helix	363-365	3
α-helix	369-371	3

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	192-195	4	13
α-helix	200-205	6
β-strand	218-221	4	13
α-helix	229-234	6
β-strand	240-244	5	13
α-helix	245-247	3
α-helix	256-269	14
β-strand	281-286	6	13
α-helix	292-301	10
α-helix	305-306	2
β-strand	307-311	5	13
β-strand	319-325	7	13
α-helix	328-332	5
α-helix	335-337	3
α-helix	340-348	9
α-helix	369-371	3

Chain D: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	629-631	3
β-strand	634-639	6	7
α-helix	645-653	9
β-strand	655	1	8
β-strand	657-663	7	7
α-helix	667-676	10
β-strand	682-683	2	7
α-helix	687-689	3
α-helix	692-698	7
β-strand	703-706	4	7
β-strand	714	1	9
α-helix	728-730	3
α-helix	731-741	11
β-strand	752-758	7	7
β-strand	761	1	9
α-helix	763-773	11
α-helix	776-777	2
β-strand	778-781	4	7
α-helix	782-784	3
β-strand	788	1	10
β-strand	791-796	6	7
α-helix	804-805	2
α-helix	815-818	4
α-helix	820	1
β-strand	824-825	2	11
β-strand	830	1	10
α-helix	837-840	4
β-strand	842	1	12
β-strand	847	1	12
β-strand	850-852	3	11
β-strand	855-857	3	11
α-helix	861-868	8
α-helix	870-871	2
α-helix	882-891	10
α-helix	895-902	8
α-helix	903-907	5
β-strand	911	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A	A, D	protein	285	Homo sapiens	Q9Y6K1 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 3-like	B, C	protein	208	Homo sapiens	Q9UJW3 (AlphaFold model)
DNA (25-mer)	E, F	DNA	25	synthetic construct

Sequence of entity 1 (A, D), FASTA

>5YX2_1 DNA (cytosine-5)-methyltransferase 3A (chains A, D)
AEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDV
RSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGD
DRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLAS
TVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERV
FGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV

Sequence of entity 2 (B, C), FASTA

>5YX2_2 DNA (cytosine-5)-methyltransferase 3-like (chains B, C)
MFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGP
FDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDV
ASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAA
KWPTKLVKNCFLPLREYFKYFSTELTSS

Sequence of entity 3 (E, F), FASTA

>5YX2_3 DNA (25-MER) (chains E, F)
GCATGUGTTCTAATTAGAACGCATG

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

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

Primary citation

Structural basis for DNMT3A-mediated de novo DNA methylation. Zhang, Z.M., Lu, R., Wang, P. et al. Nature (2018) 554:387-391. DOI 10.1038/nature25477 · 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

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