8U5H: Human DNMT3A UDR

Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome. Determined by electron microscopy at 3.23 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.23 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 13
Atoms: 13,436
Mol. weight: 251.17 kDa
Released: 12 Jun 2024

Explore 8U5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U5H contains 44 α-helices and 32 β-strands across 11 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: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	184-185	2
β-strand	186	1	1
α-helix	187	1
α-helix	200-209	10

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	174-176	3
α-helix	184-185	2
β-strand	186	1	2
α-helix	187	1

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	3
β-strand	13-16	4	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	5
β-strand	49	1	5
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-67	2	3
β-strand	68-71	4	5

Chain I: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

Chain J: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-93	11
β-strand	96-98	3	8

Chain K: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-87	8
β-strand	90	1	2
α-helix	91-96	6
β-strand	100-102	3	11

Chain M: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-118	17

Chain O: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	46-56	11
α-helix	64-75	12
β-strand	84	1	12
α-helix	86-113	28
β-strand	118-119	2	13
α-helix	121-131	11

3 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
DNA (cytosine-5)-methyltransferase 3A	A, B	protein	98	Homo sapiens	Q9Y6K1 (AlphaFold model)
nucleosome DNA	C	DNA	180	Homo sapiens
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
nucleosome DNA	H	DNA	180	Homo sapiens
Histone H3.3C	I, O	protein	136	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	J, Q	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	K, R	protein	130	Xenopus laevis	P06897
Histone H2B 1.1	M, S	protein	123	Xenopus laevis	P02281

Sequence of entity 1 (A, B), FASTA

>8U5H_1 DNA (cytosine-5)-methyltransferase 3A (chains A, B)
PEASRAVENGCCTPKEGRGAPAEAGKEQKETNIESMKMEGSRGRLRGGLGWESSLRQRPM
PRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAG

Sequence of entity 2 (C), FASTA

>8U5H_2 nucleosome DNA (chains C)
GCTCTCTACGTAAACATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGAC
AGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGG
ATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGACTTACCCACTTCG

Sequence of entity 3 (D), FASTA

>8U5H_3 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 4 (H), FASTA

>8U5H_4 nucleosome DNA (chains H)
CGAAGTGGGTAAGTCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAAT
CCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCT
GTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGATGTTTACGTAGAGAGC

Sequence of entity 5 (I, O), FASTA

>8U5H_5 Histone H3.3C (chains I, O)
MARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQRSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 6 (J, Q), FASTA

>8U5H_6 Histone H4 (chains J, Q)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 7 (K, R), FASTA

>8U5H_7 Histone H2A (chains K, R)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKC
TESSKSAKSK

Sequence of entity 8 (M, S), FASTA

>8U5H_8 Histone H2B 1.1 (chains M, S)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Primary citation

Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction. Chen, X., Guo, Y., Zhao, T. et al. Nat Commun (2024) 15:6217-6217. DOI 10.1038/s41467-024-50526-3 · 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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