8IA3

Crystal structure of human USF2 bHLHLZ domain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


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Literature

Tetramerization of upstream stimulating factor USF2 requires the elongated bent leucine zipper of the bHLH-LZ domain.

Huang, C.Xia, M.Qiao, H.Liu, Z.Lin, Y.Sun, H.Yu, B.Fang, P.Wang, J.

(2023) J Biol Chem 299: 105240-105240

  • DOI: https://doi.org/10.1016/j.jbc.2023.105240
  • Primary Citation of Related Structures:  
    8IA3

  • PubMed Abstract: 

    Upstream stimulating factors (USFs), including USF1 and USF2, are key components of the transcription machinery that recruit coactivators and histone-modifying enzymes. Using the classic basic helix-loop-helix leucine zipper (bHLH-LZ) domain, USFs bind the E-box DNA and form tetramers that promote DNA looping for transcription initiation. The structural basis by which USFs tetramerize and bind DNA, however, remains unknown. Here, we report the crystal structure of the complete bHLH-LZ domain of USF2 in complex with E-box DNA. We observed that the leucine zipper (LZ) of USF2 is longer than that of other bHLH-LZ family transcription factors and that the C-terminus of USF2 forms an additional α-helix following the LZ region (denoted as LZ-Ext). We also found the elongated LZ-Ext facilitates compact tetramer formation. In addition to the classic interactions between the basic region and DNA, we show a highly conserved basic residue in the loop region, Lys271, participates in DNA interaction. Together, these findings suggest that USF2 forms a tetramer structure with a bent elongated LZ-Ext region, providing a molecular basis for its role as a key component of the transcription machinery.


  • Organizational Affiliation

    School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Upstream stimulatory factor 2
A, B, E, F
114Homo sapiensMutation(s): 0 
Gene Names: USF2BHLHB12
UniProt & NIH Common Fund Data Resources
Find proteins for Q15853 (Homo sapiens)
Explore Q15853 
Go to UniProtKB:  Q15853
PHAROS:  Q15853
GTEx:  ENSG00000105698 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15853
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*CP*GP*GP*GP*CP*AP*CP*GP*TP*GP*AP*CP*GP*CP*GP*C)-3')
C, G
18Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*CP*GP*TP*CP*AP*CP*GP*TP*GP*CP*CP*CP*GP*TP*C)-3')
D, H
18Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.847α = 90
b = 56.951β = 90.92
c = 232.118γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21977107, 22277132, 21977108, 22277134

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references