Experimental structure

9E3U

Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker

Unclassified_Review No mapped PWWP coordinates ELECTRON MICROSCOPY

Original coordinates

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Coordinate coverage

5 chain / domain rows

Label and author chain identifiers are kept separately. Observed Cα counts refer to each mapped annotation core.

Protein	Label chain	Author chain	Domain	Observed Cα / core
DNMT3A	N	["U"]	UP:Q9Y6K1:PWWP1	0 / 59
DNMT3A	O	["Y"]	UP:Q9Y6K1:PWWP1	0 / 59
DNMT3B	I	["L"]	UP:Q9UBC3:PWWP1	0 / 59
DNMT3B	L	["V"]	UP:Q9UBC3:PWWP1	0 / 59
DNMT3B	M	["Z"]	UP:Q9UBC3:PWWP1	0 / 59

Chemical identity

2 component records

CCD	Name	Role	Full InChIKey
ZN	ZINC ION	ion/cofactor_requires_context incidental	PTFCDOFLOPIGGS-UHFFFAOYSA-N
SAH	S-ADENOSYL-L-HOMOCYSTEINE	biological cofactor functional	ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Geometry, with defined scope

Inspect 11 retained contact records

CCD / instance	Protein chain	Contact class	Minimum core / broader domain distance Å
SAH · V	DNMT3A · N	noncore contact in multidomain chain	— / —
SAH · Z	DNMT3A · O	noncore contact in multidomain chain	— / —
ZN · P	DNMT3B · L	noncore contact in multidomain chain	— / —
ZN · Q	DNMT3B · L	noncore contact in multidomain chain	— / —
ZN · R	DNMT3B · L	noncore contact in multidomain chain	— / —
ZN · S	DNMT3A · N	noncore contact in multidomain chain	— / —
ZN · T	DNMT3A · N	noncore contact in multidomain chain	— / —
ZN · U	DNMT3A · N	noncore contact in multidomain chain	— / —
ZN · W	DNMT3A · O	noncore contact in multidomain chain	— / —
ZN · X	DNMT3A · O	noncore contact in multidomain chain	— / —
ZN · Y	DNMT3A · O	noncore contact in multidomain chain	— / —

Histone H3.2 · histone or histone peptide · label chains ["A","E"]

Histone H4 · histone or histone peptide · label chains ["B","F"]

Histone H2A · histone or histone peptide · label chains ["C","G"]

Histone H2B · histone or histone peptide · label chains ["D","H"]

Isoform 3 of DNA (cytosine-5)-methyltransferase 3B · protein/peptide · label chains ["I","L","M"]

DNA (165-MER) · nucleic acid · label chains ["J"]

DNA (165-MER) · nucleic acid · label chains ["K"]

DNA (cytosine-5)-methyltransferase 3A · protein/peptide · label chains ["N","O"]

Source interpretation

This entry was included in all-entry coordinate/contact calculations but not in the 36-entry focused structural sample.