6U90: DNMT3B(N779A)-DNMT3L

Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA. Determined by X-ray diffraction at 3.0 Å resolution. Released 10 Jun 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,631
Mol. weight: 130.97 kDa
Ligands: SAH
Released: 10 Jun 2020

Explore 6U90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U90 contains 61 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	564-566	3
β-strand	575-580	6	1
α-helix	586-594	9
β-strand	596	1	2
β-strand	598-604	7	1
α-helix	608-618	11
β-strand	622-624	3	1
α-helix	628-630	3
α-helix	633-639	7
β-strand	644-648	5	1
α-helix	671-682	12
α-helix	684-685	2
β-strand	693-699	7	1
α-helix	704-714	11
α-helix	718	1
β-strand	719-722	4	1
α-helix	723-725	3
β-strand	729	1	3
β-strand	732-737	6	1
α-helix	745-746	2
α-helix	756-759	4
β-strand	765-766	2	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	799-801	3
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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	184-186	3
α-helix	188-190	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	256-270	15
β-strand	281-286	6	6
α-helix	292-302	11
β-strand	307-309	3	6
β-strand	313	1	7
β-strand	316	1	7
β-strand	321-325	5	6
α-helix	328-332	5
α-helix	340-350	11
α-helix	365-367	3
α-helix	369-374	6

Chain C: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	188-190	3
β-strand	192-195	4	8
α-helix	200-205	6
β-strand	218-221	4	8
α-helix	229-234	6
β-strand	240-244	5	8
α-helix	245-247	3
α-helix	256-270	15
β-strand	281-286	6	8
α-helix	292-302	11
α-helix	305-306	2
β-strand	307-311	5	8
β-strand	319-325	7	8
α-helix	328-331	4
α-helix	340-350	11
α-helix	361-368	8
α-helix	369-373	5

Chain D: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	564-566	3
β-strand	575-580	6	9
α-helix	586-593	8
β-strand	596	1	10
β-strand	598-604	7	9
α-helix	608-618	11
β-strand	622-624	3	9
α-helix	628-630	3
α-helix	633-639	7
β-strand	644-647	4	9
α-helix	671-682	12
α-helix	684-685	2
β-strand	693-699	7	9
α-helix	704-714	11
β-strand	719-722	4	9
α-helix	723-725	3
β-strand	729	1	11
β-strand	732-737	6	9
α-helix	745-746	2
α-helix	756-759	4
β-strand	765-766	2	12
β-strand	771	1	11
α-helix	772-774	3
α-helix	778-781	4
β-strand	783	1	13
β-strand	788	1	13
β-strand	791-793	3	12
β-strand	796-798	3	12
α-helix	799-801	3
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	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3B	A, D	protein	291	Homo sapiens	Q9UBC3 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 3-like	B, C	protein	209	Homo sapiens	Q9UJW3 (AlphaFold model)
CpGpT DNA (25-MER)	E, F	DNA	25	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6U90_1 DNA (cytosine-5)-methyltransferase 3B (chains A, D)
LYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNI
KYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYS
RPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGM
NRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSASIKQGKNQLFPVVMNGKEDVLWC
TELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

Sequence of entity 2 (B, C), FASTA

>6U90_2 DNA (cytosine-5)-methyltransferase 3-like (chains B, C)
MFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGP
FDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDV
ASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAA
KWPTKLVKNCFLPLREYFKYFSTELTSSL

Sequence of entity 3 (E, F), FASTA

>6U90_3 CpGpT 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

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Gao, L. To be published.

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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