ISDA: 6V8W

Deposition Date 2019-12-12

Release Date 2020-01-15

Last Version Date 2025-10-22

Entry Detail

PDB ID:

6V8W

Keywords:

PROTEIN BINDING

Title:

CDYL2 chromodomain in complex with a synthetic peptide

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.27

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Chromodomain Y-like protein 2
Gene (Uniprot):CDYL2
Chain IDs:A, C (auth: B), E (auth: C), G (auth: D), I (auth: E), K (auth: F), M (auth: G), O (auth: H), Q (auth: I), S (auth: J), U (auth: K), W (auth: L), Y (auth: M), AA (auth: N), CA (auth: O), EA (auth: P), GA (auth: Q), IA (auth: R), KA (auth: S), MA (auth: T), OA (auth: U), QA (auth: V), SA (auth: W), UA (auth: X), WA (auth: Y), YA (auth: Z)
Chain Length:62
Number of Molecules:26
Biological Source:Homo sapiens

UniProt ID:Q8N8U2 Pfam ID:PF00385

Polymer Type:polypeptide(L)
Molecule:IVA-PHE-ALA-PHE-5T3-SER-NH2
Chain IDs:B (auth: AA), D (auth: BB), F (auth: CC), H (auth: DD), J (auth: EE), L (auth: FF), N (auth: GG), P (auth: HH), R (auth: II), T (auth: JJ), V (auth: KK), X (auth: LL), Z (auth: MM), BA (auth: NN), DA (auth: OO), FA (auth: PP), HA (auth: QQ), JA (auth: RR), LA (auth: SS), NA (auth: TT), PA (auth: UU), RA (auth: VV), TA (auth: WW), VA (auth: XX), XA (auth: YY), ZA (auth: ZZ)
Chain Length:7
Number of Molecules:26
Biological Source:synthetic construct

Ligand Molecules

UNX

Primary Citation

Structural Basis for the Binding Selectivity of Human CDY Chromodomains.

Dong, C, Liu, Y, Lyu, T.J, Beldar, S, Lamb, K.N, Tempel, W, Li, Y, Li, Z, James, L.I, Qin, S, Wang, Y, Min, J.Show

Cell Chem Biol 27 827 838.e7 (2020)

PMID: 32470319 DOI: 10.1016/j.chembiol.2020.05.007

Abstact

The CDY (chromodomain on the Y) proteins play an essential role in normal spermatogenesis and brain development. Dysregulation of their expression has been linked to male infertility and various neurological diseases. Like the chromodomains of HP1 and Polycomb, the CDY chromodomains also recognize the lysine-methylated ARKS motif embedded in histone and non-histone proteins. Interestingly, the CDY chromodomains exhibit different binding preferences for the lysine-methylated ARKS motif in different sequence contexts. Here, we present the structural basis for selective binding of CDY1 to H3K9me3 and preferential binding of CDYL2 to H3tK27me3 over H3K27me3. In addition, we use a CDYL1/2-selective compound, UNC4850, to gain further insight into the molecular mechanisms underlying CDYL2 binding specificity. Our work also provides critical implications that CDYL1b's role in the regulation of neural development is dependent on its recognition of the lysine-methylated ARKS motif.

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Primary Citation of related structures

Abstact

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