7VN8

Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning GTCACGTGAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout.

Nosaki, S.Mitsuda, N.Sakamoto, S.Kusubayashi, K.Yamagami, A.Xu, Y.Bui, T.B.C.Terada, T.Miura, K.Nakano, T.Tanokura, M.Miyakawa, T.

(2022) Nat Plants 8: 1440-1452

  • DOI: https://doi.org/10.1038/s41477-022-01289-6
  • Primary Citation of Related Structures:  
    7VN2, 7VN3, 7VN4, 7VN5, 7VN6, 7VN7, 7VN8

  • PubMed Abstract: 

    BRZ-INSENSITIVE-LONG 1 (BIL1)/BRASSINAZOLE-RESISTANT 1 (BZR1) and its homologues are plant-specific transcription factors that convert the signalling of the phytohormones brassinosteroids (BRs) to transcriptional responses, thus controlling various physiological processes in plants. Although BIL1/BZR1 upregulates some BR-responsive genes and downregulates others, the molecular mechanism underlying the dual roles of BIL1/BZR1 is still poorly understood. Here we show that BR-responsive transcriptional repression by BIL1/BZR1 requires the tight binding of BIL1/BZR1 alone to the 10 bp elements of DNA fragments containing the known 6 bp core-binding motifs at the centre. Furthermore, biochemical and structural evidence demonstrates that the selectivity for two nucleobases flanking the core motifs is realized by the DNA shape readout of BIL1/BZR1 without direct recognition of the nucleobases. These results elucidate the molecular and structural basis of transcriptional repression by BIL1/BZR1 and contribute to further understanding of the dual roles of BIL1/BZR1 in BR-responsive gene regulation.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1A [auth C],
B [auth D],
E [auth A],
F [auth B]
439Serratia sp. FS14Arabidopsis thaliana
This entity is chimeric
Mutation(s): 8 
Gene Names: malEJW3994BZR1BIS2At1g75080F9E10_7
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q8S307 (Arabidopsis thaliana)
Explore Q8S307 
Go to UniProtKB:  Q8S307
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8S307P0AEX9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*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-glucopyranoseI [auth K],
J [auth L],
K [auth M],
L [auth N]
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
M [auth C]
N [auth C]
O [auth D]
P [auth D]
Q [auth D]
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth D],
R [auth G],
S [auth H],
T [auth A],
U [auth A],
V [auth A],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.402α = 90
b = 94.47β = 100.65
c = 112.941γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17H05835, 19H04855, 19K23658, 21H02114
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101077

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-01-11
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description