7V9G

Native BEN4 domain of protein Bend3 with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.

(2022) Science 375: 1053-1058

  • DOI: https://doi.org/10.1126/science.abm0730
  • Primary Citation of Related Structures:  
    7V9F, 7V9G, 7V9H, 7V9I

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BEN domain-containing protein 3
A, D, G, J
114Mus musculusMutation(s): 0 
Gene Names: Bend3
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PAL0 (Mus musculus)
Explore Q6PAL0 
Go to UniProtKB:  Q6PAL0
IMPC:  MGI:2677212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PAL0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
B, E, H, K
16Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
C, F, I, L
16Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.484α = 90
b = 200.484β = 90
c = 151.274γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2019YFA0508900, 2017YFA0504202
National Science Foundation (NSF, China)China31991162, 31521002
Chinese Academy of SciencesChinaXDB 37010100

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-16
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection, Refinement description