6KDA: Human DNMT3B-DNMT3L

Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site. Determined by X-ray diffraction at 2.91 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 9,004
Mol. weight: 128.85 kDa
Ligands: SAH
Released: 19 Feb 2020

Explore 6KDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KDA contains 57 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: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	575-580	6	1
α-helix	586-594	9
β-strand	596	1	2
β-strand	598-604	7	1
α-helix	608-617	10
β-strand	623-624	2	1
α-helix	628-630	3
α-helix	633-639	7
β-strand	644-647	4	1
α-helix	671-682	12
α-helix	684-685	2
β-strand	693-699	7	1
α-helix	704-713	10
α-helix	717-718	2
β-strand	719-722	4	1
α-helix	723-725	3
β-strand	729	1	3
β-strand	732-737	6	1
α-helix	756-759	4
β-strand	764-766	3	4
β-strand	771	1	3
α-helix	772-774	3
α-helix	778-781	4
β-strand	783	1	5
β-strand	788	1	5
β-strand	791-793	3	4
β-strand	796-798	3	4
α-helix	802-809	8
α-helix	811-812	2
α-helix	823-831	9
α-helix	836-843	8
α-helix	844-848	5
β-strand	852	1	2

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	180-183	4
β-strand	188	1	6
β-strand	192-195	4	7
α-helix	200-203	4
α-helix	204-206	3
β-strand	218-221	4	7
α-helix	224-226	3
α-helix	229-234	6
β-strand	240-244	5	7
α-helix	245-247	3
α-helix	256-270	15
α-helix	272-273	2
β-strand	281-286	6	7
α-helix	292-301	10
β-strand	307-311	5	7
β-strand	319-325	7	7
α-helix	340-350	11
α-helix	361-365	5
α-helix	366-373	8
β-strand	375	1	6

Chain C: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	180-183	4
β-strand	188	1	8
β-strand	192-195	4	9
α-helix	200-203	4
α-helix	204-206	3
β-strand	218-221	4	9
α-helix	224-226	3
α-helix	229-235	7
β-strand	240-244	5	9
α-helix	245-247	3
α-helix	256-270	15
α-helix	272-273	2
β-strand	281-286	6	9
α-helix	292-301	10
β-strand	307-311	5	9
β-strand	319-325	7	9
α-helix	340-349	10
α-helix	361-366	6
α-helix	369-373	5
β-strand	375	1	8

Chain D: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	575-580	6	10
α-helix	586-593	8
β-strand	596	1	11
β-strand	598-604	7	10
α-helix	608-617	10
β-strand	623-624	2	10
α-helix	628-630	3
α-helix	633-639	7
β-strand	644-648	5	10
α-helix	669-671	3
α-helix	672-682	11
β-strand	693-699	7	10
α-helix	704-713	10
α-helix	717-718	2
β-strand	719-722	4	10
α-helix	723-725	3
β-strand	729	1	12
β-strand	732-737	6	10
α-helix	756-759	4
β-strand	764-766	3	13
β-strand	771	1	12
α-helix	772-774	3
β-strand	783	1	14
β-strand	788	1	14
β-strand	791-793	3	13
β-strand	796-798	3	13
α-helix	802-808	7
α-helix	811-812	2
α-helix	823-831	9
α-helix	836-843	8
α-helix	844-848	5
β-strand	852	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3B	A, D	protein	286	Homo sapiens	Q9UBC3 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 3-like	B, C	protein	204	Homo sapiens	Q9UJW3 (AlphaFold model)
DNA (25-mer)	E, F	DNA	25	synthetic construct

Sequence of entity 1 (A, D), FASTA

>6KDA_1 DNA (cytosine-5)-methyltransferase 3B (chains A, D)
GHMRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVND
VRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEG
DDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVI
ASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELER
IFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

Sequence of entity 2 (B, C), FASTA

>6KDA_2 DNA (cytosine-5)-methyltransferase 3-like (chains B, C)
GHMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEW
GPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDL
DVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKL
AAKWPTKLVKNCFLPLREYFKYFS

Sequence of entity 3 (E, F), FASTA

>6KDA_3 DNA (25-MER) (chains E, F)
GAATTCGGAAAAATTTTTCCGAATT

Ligands and cofactors

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

Primary citation

Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Lin, C.C., Chen, Y.P., Yang, W.Z. et al. Nucleic Acids Res (2020) 48:3949-3961. DOI 10.1093/nar/gkaa111 · 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
7O45 2.1 Å, Crystal structure of ADD domain of the human DNMT3B methyltransferase
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

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