7YUL

Crystal structure of human BEND6 BEN domain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights into DNA recognition by the BEN domain of the transcription factor BANP.

Liu, K.Zhang, J.Xiao, Y.Yang, A.Song, X.Li, Y.Chen, Y.Hughes, T.R.Min, J.

(2023) J Biol Chem 299: 104734-104734

  • DOI: https://doi.org/10.1016/j.jbc.2023.104734
  • Primary Citation of Related Structures:  
    7YUG, 7YUK, 7YUL, 7YUN, 8HTX

  • PubMed Abstract: 

    The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA sequence or an AAA-containing matrix attachment regions DNA sequence. Consistent with these in vivo observations, we identified an optimal DNA-binding sequence of AAATCTCG by protein binding microarray, which was also confirmed by our isothermal titration calorimetry and mutagenesis results. We then determined crystal structures of the BANP BEN domain in apo form and in complex with a CGCG-containing DNA, respectively, which revealed that the BANP BEN domain mainly used the electrostatic interactions to bind DNA with some base-specific interactions with the TC motifs. Our isothermal titration calorimetry results also showed that BANP bound to unmethylated and methylated DNAs with comparable binding affinities. Our complex structure of BANP-mCGCG revealed that the BANP BEN domain bound to the unmethylated and methylated DNAs in a similar mode and cytosine methylation did not get involved in binding, which is also consistent with our observations from the complex structures of the BEND6 BEN domain with the CGCG or CGmCG DNAs. Taken together, our results further elucidate the elements important for DNA recognition and transcriptional regulation by the BANP BEN domain-containing transcription factor.


  • Organizational Affiliation

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China. Electronic address: keliu2015@ccnu.edu.cn.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BEN domain-containing protein 6103Homo sapiensMutation(s): 0 
Gene Names: BEND6C6orf65
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SZJ8 (Homo sapiens)
Explore Q5SZJ8 
Go to UniProtKB:  Q5SZJ8
PHAROS:  Q5SZJ8
GTEx:  ENSG00000151917 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SZJ8
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')B [auth C]12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOA
Query on GOA

Download Ideal Coordinates CCD File 
C
GLYCOLIC ACID
C2 H4 O3
AEMRFAOFKBGASW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.092α = 90
b = 39.514β = 90
c = 43.719γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770834

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Derived calculations
  • Version 1.2: 2023-05-24
    Changes: Database references
  • Version 1.3: 2023-05-31
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2023-11-29
    Changes: Refinement description