ISDA

Deposition Date 2021-08-25

Release Date 2022-02-16

Last Version Date 2024-10-16

Entry Detail

PDB ID:

7V9F

Keywords:

DNA BINDING PROTEIN/DNA

Title:

Selenomethionine mutant (L740Sem) of BEN4 domain of protein Bend3 with DNA

Biological Source:

Source Organism:

Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.50 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 62 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:BEN domain-containing protein 3
Gene (Uniprot):Bend3
Chain IDs:A
Chain Length:114
Number of Molecules:1
Biological Source:Mus musculus

UniProt ID:Q6PAL0 Pfam ID:PF10523

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
Chain IDs:B
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
Chain IDs:C
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	A	MET	modified residue

Ligand Molecules

CIT

Primary Citation

Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.

Zhang, J, Zhang, Y, You, Q, Huang, C, Zhang, T, Wang, M, Zhang, T, Yang, X, Xiong, J, Li, Y, Liu, C.P, Zhang, Z, Xu, R.M, Zhu, B.Show

Science 375 1053 1058 (2022)

PMID: 35143257 DOI: 10.1126/science.abm0730

Abstact

Bivalent genes are ready for activation upon the arrival of developmental cues. Here, we report that BEND3 is a CpG island (CGI)-binding protein that is enriched at regulatory elements. The cocrystal structure of BEND3 in complex with its target DNA reveals the structural basis for its DNA methylation-sensitive binding property. Mouse embryos ablated of Bend3 died at the pregastrulation stage. Bend3 null embryonic stem cells (ESCs) exhibited severe defects in differentiation, during which hundreds of CGI-containing bivalent genes were prematurely activated. BEND3 is required for the stable association of polycomb repressive complex 2 (PRC2) at bivalent genes that are highly occupied by BEND3, which suggests a reining function of BEND3 in maintaining high levels of H3K27me3 at these bivalent genes in ESCs to prevent their premature activation in the forthcoming developmental stage.

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Protein

Chemical

Disease

Primary Citation of related structures