6V2H: CDYL2

Crystal structure of CDYL2 in complex with H3tK27me3. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 3,371
Mol. weight: 52.68 kDa
Ligands: NI
Released: 25 Dec 2019

Explore 6V2H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V2H contains 20 α-helices and 40 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, C, E, G, I and K: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	9-17	9	2
β-strand	23-29	7	2
α-helix	34-36	3
β-strand	38-41	4	2
α-helix	42-44	3
β-strand	45-46	2	1
α-helix	49-56	8

Chains B and J: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	24-26	3	1

Chains D and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	24-26	3	4

Chains F and H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	24-26	3	1
α-helix	27-28	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromodomain Y-like protein 2	A, C, E, G, I, K	protein	62	Homo sapiens	Q8N8U2 (AlphaFold model)
H3tK27me3	B, D, F, H, J, L	protein	14	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>6V2H_1 Chromodomain Y-like protein 2 (chains A, C, E, G, I, K)
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHM
SK

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>6V2H_2 H3tK27me3 (chains B, D, F, H, J, L)
XATKVARKSAPATX

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	6

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

Primary citation

Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Dong, C., Liu, Y., Lyu, T.J. et al. Cell Chem Biol (2020) 27:827-838.e7. DOI 10.1016/j.chembiol.2020.05.007 · PubMed

Other PDB entries of the same protein (UniProt Q8N8U2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SP6 1.45 Å, Complex structure of CDYL2 with an antagonist
4HAE 2.0 Å, Crystal structure of the CDYL2-chromodomain
5JJZ 2.0 Å, Chromo domain of human Chromodomain Protein, Y-Like 2
6V2D 2.1 Å, Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866
6V3N 2.7 Å, Crystal structure of CDYL2 in complex with H3K27me3
6V8W 2.8 Å, CDYL2 chromodomain in complex with a synthetic peptide
2MJ8 Solution structure of CDYL2 chromodomain

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