6PA7: Human DNMT3A2-DNMT3B3 complex

The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Determined by electron microscopy at 2.94 Å resolution. Released 17 Jun 2020.

Method: Electron microscopy
Resolution: 2.94 Å
Organisms: Xenopus laevis, synthetic construct, Homo sapiens
Chains: 14
Atoms: 21,019
Mol. weight: 541.07 kDa
Ligands: SAH
Released: 17 Jun 2020

Explore 6PA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PA7 contains 94 α-helices and 60 β-strands across 12 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.

Chains A and E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-56	14
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chains C and G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-119	18

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-43	9
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-119	18

Chains K and P: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	619-626	8
α-helix	628-630	3
β-strand	634-638	5	11
α-helix	645-652	8
β-strand	657-663	7	11
α-helix	667-677	11
β-strand	681-684	4	11
α-helix	687-689	3
α-helix	692-697	6
β-strand	703-707	5	11
α-helix	730-741	12
β-strand	752-758	7	11
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	12
β-strand	791-796	6	11
β-strand	823-825	3	13
β-strand	830-831	2	12
β-strand	850-852	3	13
β-strand	856-857	2	13
α-helix	858-860	3
α-helix	861-867	7
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

Chain N: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	545-548	4
α-helix	554	1
β-strand	555-556	2	14
β-strand	557-560	4	15
α-helix	566-572	7
β-strand	578-580	3	14
β-strand	582-583	2	16
α-helix	589-597	9
β-strand	603-604	2	16
α-helix	608-610	3
α-helix	613-618	6
β-strand	624-627	4	15
α-helix	648-662	15
β-strand	673-678	6	15
α-helix	684-694	11
β-strand	699-702	4	15
β-strand	712-717	6	15
α-helix	731-734	4
α-helix	741-743	3
α-helix	744-748	5
α-helix	756-759	4
α-helix	761-763	3

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
DNA (167-mer)	I	DNA	167	synthetic construct
DNA (167-mer)	J	DNA	167	synthetic construct
DNA (cytosine-5)-methyltransferase 3A	K, P	protein	689	Homo sapiens	Q9Y6K1
DNA (cytosine-5)-methyltransferase 3B	N, S	protein	770	Homo sapiens	Q9UBC3

Sequence of entity 1 (A, E), FASTA

>6PA7_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6PA7_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6PA7_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>6PA7_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>6PA7_5 DNA (167-MER) (chains I)
ATCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGGCGGCCGAT

Sequence of entity 6 (J), FASTA

>6PA7_6 DNA (167-MER) (chains J)
ATCGGCCGCCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGAT

Sequence of entity 7 (K, P), FASTA

>6PA7_7 DNA (cytosine-5)-methyltransferase 3A (chains K, P)
MNAVEENQGPGESQKVEEASPPAVQQPTDPASPTVATTPEPVGSDAGDKNATKAGDDEPE
YEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEK
LMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRAGKLFPVCHDSDESDTAKAVEVQN
KPMIEWALGGFQPSGPKGLEPPEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTAE
KPKVKEIIDERTRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLE
CAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNC
YMCGHKGTYGLLRRREDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGI
ATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDL
VIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGV
SDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGR
IAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRL
ARQRLLGRSWSVPVIRHLFAPLKEYFACV

Sequence of entity 8 (N, S), FASTA

>6PA7_8 DNA (cytosine-5)-methyltransferase 3B (chains N, S)
MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV
SSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS
PRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT
PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP
AMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK
AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPENKTR
RRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGR
KNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFC
VECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEA
PKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEG
NIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLN
YSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLP
GMNRIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

Ligands and cofactors

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

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

Primary citation

Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Xu, T.H., Liu, M., Zhou, X.E. et al. Nature (2020) 586:151-155. DOI 10.1038/s41586-020-2747-1 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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