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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41477-018-0255-1

  • 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, dist ...

    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.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. amtanok@mail.ecc.u-tokyo.ac.jp.,Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
C, D, A, B
453Escherichia coli O157:H7Arabidopsis thaliana
This entity is chimeric
Mutation(s): 8 
Gene Names: malE, BZR1 (BIS2)
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for Q8S307 (Arabidopsis thaliana)
Go to UniProtKB:  Q8S307
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')G,H,E,F15synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A, B, C, D
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.701α = 90.00
b = 92.603β = 100.42
c = 111.967γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references