5ZD4

Crystal structure of MBP-fused BIL1/BZR1 in complex with double-stranded DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Structural basis for brassinosteroid response by BIL1/BZR1.

Nosaki, S., Miyakawa, T., Xu, Y., Nakamura, A., Hirabayashi, K., Asami, T., Nakano, T., Tanokura, M.

(2018) Nat Plants 4: 771-776

  • DOI: https://doi.org/10.1038/s41477-018-0255-1
  • Primary Citation of Related Structures:  
    5ZD4

  • PubMed Abstract: 

    BRZ-INSENSITIVE-LONG HYPOCOTYL 1 (BIL1)/BRASSINAZOLE-RESISTANT 1 (BZR1) is a master transcription factor of brassinosteroid (BR) signalling. The varieties of nucleobase recognition of the NN-BRRE-core motif (NNCGTG), one of variant G-box motifs, distinguish BIL1/BZR1 from basic helix-loop-helix transcription factors, underlying the specific regulation of BR-responsive genes. Here, we show the non-canonical bHLH dimer formation of BIL1/BZR1 to optimize the interaction network with DNA and the orientation of a key residue for NN-BRRE-core motif recognition.

    • Organizational Affiliation: 

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1A [auth C],
B [auth D],
E [auth A],
F [auth B]		453Escherichia coli O157:H7, Arabidopsis thaliana
This entity is chimeric		Mutation(s): 8 
Gene Names: malE, Z5632, ECs5017, BZR1, BIS2, At1g75080, F9E10_7
UniProt
Find proteins for Q8S307 (Arabidopsis thaliana)
Explore Q8S307 
Go to UniProtKB:  Q8S307
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8S307P0AEY0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')C [auth G],
D [auth H],
G [auth E],
H [auth F]		15synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.701α = 90
b = 92.603β = 100.42
c = 111.967γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary