2QRV: Dnmt3a-Dnmt3L C-terminal domain complex

Structure of Dnmt3a-Dnmt3L C-terminal domain complex. Determined by X-ray diffraction at 2.89 Å resolution. Released 4 Dec 2007.

Method: X-ray diffraction
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,657
Mol. weight: 244.15 kDa
Ligands: SAH
Released: 4 Dec 2007

Explore 2QRV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QRV contains 103 α-helices and 86 β-strands across 8 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	630-635	6	1
α-helix	641-648	8
β-strand	651	1	2
β-strand	653-659	7	1
α-helix	663-672	10
β-strand	677-680	4	1
α-helix	683-685	3
α-helix	688-693	6
β-strand	699-702	4	1
α-helix	707-709	3
β-strand	710	1	3
α-helix	726-737	12
α-helix	739-740	2
β-strand	748-754	7	1
β-strand	757	1	3
α-helix	759-769	11
β-strand	776-777	2	1
α-helix	778-780	3
β-strand	784	1	4
β-strand	787-792	6	1
α-helix	811-813	3
α-helix	816	1
β-strand	820-821	2	5
β-strand	826	1	4
β-strand	846-848	3	5
β-strand	851-853	3	5
α-helix	854-856	3
α-helix	857-864	8
α-helix	878-886	9
α-helix	891-898	8
α-helix	899-904	6
β-strand	907	1	2

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	179-181	3
α-helix	184-186	3
α-helix	188-190	3
β-strand	192-195	4	6
β-strand	218-221	4	6
α-helix	229-234	6
β-strand	240-244	5	6
α-helix	245-247	3
α-helix	257-270	14
β-strand	281-286	6	6
α-helix	292-302	11
β-strand	307-308	2	6
β-strand	322-325	4	6
α-helix	340-351	12
α-helix	362-365	4
α-helix	369-373	5

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	179-181	3
α-helix	184-186	3
α-helix	188-191	4
β-strand	192-195	4	7
β-strand	218-221	4	7
α-helix	229-234	6
β-strand	240-244	5	7
α-helix	245-247	3
α-helix	257-269	13
β-strand	281-286	6	7
α-helix	292-302	11
β-strand	307-308	2	7
β-strand	322-325	4	7
α-helix	340-351	12
α-helix	362-365	4
α-helix	369-373	5

Chain D: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	630-635	6	8
α-helix	641-648	8
β-strand	651	1	9
β-strand	653-659	7	8
α-helix	663-672	10
β-strand	677-680	4	8
α-helix	683-685	3
α-helix	688-693	6
β-strand	699-702	4	8
α-helix	707-709	3
β-strand	710	1	10
α-helix	726-737	12
α-helix	739-740	2
β-strand	748-754	7	8
β-strand	757	1	10
α-helix	759-768	10
β-strand	776-777	2	8
α-helix	778-780	3
β-strand	784	1	11
β-strand	787-792	6	8
α-helix	811-814	4
α-helix	816	1
β-strand	819-821	3	12
β-strand	826	1	11
β-strand	846-848	3	12
β-strand	851-853	3	12
α-helix	857-864	8
α-helix	866-867	2
α-helix	878-886	9
α-helix	891-898	8
α-helix	899-904	6
β-strand	907	1	9

Chain E: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	630-635	6	13
α-helix	641-648	8
β-strand	651	1	14
β-strand	653-659	7	13
α-helix	663-672	10
β-strand	677-680	4	13
α-helix	683-685	3
α-helix	688-693	6
β-strand	699-702	4	13
α-helix	707-709	3
β-strand	710	1	15
α-helix	726-737	12
α-helix	739-740	2
β-strand	748-754	7	13
β-strand	757	1	15
α-helix	759-769	11
β-strand	776-777	2	13
α-helix	778-780	3
β-strand	784	1	16
β-strand	787-792	6	13
α-helix	811-814	4
β-strand	820-821	2	17
β-strand	826	1	16
β-strand	846-847	2	17
β-strand	852-853	2	17
α-helix	857-863	7
α-helix	866-867	2
α-helix	878-887	10
α-helix	891-898	8
α-helix	899-904	6
β-strand	907	1	14

Chain F: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	179-181	3
α-helix	184-186	3
α-helix	187-190	4
β-strand	192-195	4	18
β-strand	218-221	4	18
α-helix	229-234	6
β-strand	240-244	5	18
α-helix	245-247	3
α-helix	257-269	13
β-strand	281-286	6	18
α-helix	292-302	11
β-strand	307-308	2	18
β-strand	322-325	4	18
α-helix	340-351	12
α-helix	362-365	4
α-helix	369-373	5
α-helix	376-378	3

Chain G: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	184-186	3
α-helix	188-190	3
β-strand	192-195	4	19
β-strand	218-221	4	19
α-helix	229-234	6
β-strand	240-244	5	19
α-helix	245-247	3
α-helix	257-269	13
β-strand	281-286	6	19
α-helix	292-302	11
β-strand	307-308	2	19
β-strand	322-325	4	19
α-helix	340-351	12
α-helix	362-365	4
α-helix	369-373	5

Chain H: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	630-635	6	20
α-helix	641-648	8
β-strand	653-659	7	20
α-helix	663-672	10
β-strand	677-680	4	20
α-helix	683-685	3
α-helix	688-693	6
β-strand	699-702	4	20
α-helix	707-709	3
β-strand	710	1	21
α-helix	726-737	12
α-helix	739-740	2
β-strand	748-754	7	20
β-strand	757	1	21
α-helix	759-769	11
β-strand	776-777	2	20
α-helix	778-780	3
β-strand	784	1	22
β-strand	787-792	6	20
α-helix	811-814	4
α-helix	816	1
β-strand	820-821	2	23
β-strand	826	1	22
β-strand	846-847	2	23
β-strand	852-853	2	23
α-helix	854-856	3
α-helix	857-864	8
α-helix	878-887	10
α-helix	891-897	7
α-helix	899-903	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A	A, D, E, H	protein	295	Homo sapiens	Q9Y6K1 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 3-like	B, C, F, G	protein	230	Homo sapiens	Q9UJW3 (AlphaFold model)

Sequence of entity 1 (A, D, E, H), FASTA

>2QRV_1 DNA (cytosine-5)-methyltransferase 3A (chains A, D, E, H)
MGHHHHHHMPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRH
QGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRL
LHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGN
LPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKED
ILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV

Sequence of entity 2 (B, C, F, G), FASTA

>2QRV_2 DNA (cytosine-5)-methyltransferase 3-like (chains B, C, F, G)
GSMWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPG
QLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGS
PRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWA
LVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFSTELTSSL

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4

Primary citation

Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Jia, D., Jurkowska, R.Z., Zhang, X. et al. Nature (2007) 449:248-251. DOI 10.1038/nature06146 · 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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