7X9D: DNMT3B

Name: PDB 7X9D: DNMT3B in complex with harmine
Published: 2023-03-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

DNMT3B in complex with harmine. Determined by X-ray diffraction at 3.08 Å resolution. Released 15 Mar 2023.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,701
Mol. weight: 113.11 kDa
Ligands: HRM
Released: 15 Mar 2023

Explore 7X9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7X9D contains 57 α-helices and 40 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	575-580	6	1
α-helix	586-593	8
β-strand	596	1	2
β-strand	598-604	7	1
α-helix	608-616	9
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	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	745-746	2
α-helix	756-759	4
β-strand	765-766	2	4
β-strand	771	1	3
α-helix	772-774	3
β-strand	791-793	3	4
β-strand	796-798	3	4
α-helix	802-808	7
α-helix	811-812	2
α-helix	823-831	9
α-helix	836-843	8
α-helix	844-849	6
β-strand	852	1	2

Chain B: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	184-186	3
α-helix	188-190	3
β-strand	192-195	4	5
α-helix	200-205	6
β-strand	218-221	4	5
α-helix	229-234	6
β-strand	240-244	5	5
α-helix	251-252	2
α-helix	256-270	15
α-helix	272-273	2
β-strand	281-286	6	5
α-helix	292-301	10
β-strand	307-313	7	5
β-strand	316-325	10	5
α-helix	331-333	3
α-helix	340-349	10
α-helix	362-365	4
α-helix	366-373	8

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	192-196	5	6
α-helix	200-206	7
β-strand	218-221	4	6
α-helix	229-235	7
β-strand	240-244	5	6
α-helix	245-247	3
α-helix	256-270	15
α-helix	272-273	2
β-strand	281-286	6	6
α-helix	292-302	11
β-strand	307-313	7	6
β-strand	316-325	10	6
α-helix	328-330	3
α-helix	340-353	14
α-helix	362-365	4
α-helix	366-371	6

Chain D: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	575-580	6	7
α-helix	586-593	8
β-strand	596	1	8
β-strand	598-604	7	7
α-helix	608-617	10
β-strand	622-625	4	7
α-helix	628-630	3
α-helix	633-639	7
β-strand	644-647	4	7
α-helix	667-670	4
α-helix	671-682	12
α-helix	684-685	2
β-strand	693-699	7	7
α-helix	704-714	11
α-helix	718	1
β-strand	719-722	4	7
α-helix	723-725	3
β-strand	729	1	9
β-strand	732-737	6	7
α-helix	745-746	2
α-helix	756-759	4
β-strand	765-766	2	10
β-strand	771	1	9
α-helix	772-774	3
β-strand	791-793	3	10
β-strand	796-798	3	10
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	8

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)

Sequence of entity 1 (A, D), FASTA

>7X9D_1 DNA (cytosine-5)-methyltransferase 3B (chains A, D)
GHMRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVND
VRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEG
DDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVI
ASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELER
IFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

Sequence of entity 2 (B, C), FASTA

>7X9D_2 DNA (cytosine-5)-methyltransferase 3-like (chains B, C)
GHMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEW
GPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDL
DVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKL
AAKWPTKLVKNCFLPLREYFKYFS

Ligands and cofactors

ID	Name	Formula	Copies
HRM	7-methoxy-1-methyl-9H-beta-carboline	C13 H12 N2 O	2

Primary citation

Mechanistic Insights into Harmine-Mediated Inhibition of Human DNA Methyltransferases and Prostate Cancer Cell Growth. Cho, C.C., Lin, C.J., Huang, H.H. et al. ACS Chem Biol (2023) 18:1335-1350. DOI 10.1021/acschembio.3c00065 · 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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