5ZD4 | pdb_00005zd4

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

• PDB DOI: https://doi.org/10.2210/pdb5ZD4/pdb
• NAKB: 5ZD4

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli O157:H7, Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-02-22 Released: 2018-08-29 
• Deposition Author(s): Nosaki, S., Miyakawa, T., Xu, Y., Nakamura, A., Hirabayashi, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.244 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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

• PubMed: 30287951 
• DOI: https://doi.org/10.1038/s41477-018-0255-1
• Primary Citation 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.

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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.
Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 219.45 kDa 
• Atom Count: 15,004 
• Modeled Residue Count: 1,778 
• Deposited Residue Count: 1,872 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1	A [auth C], B [auth D], E [auth A], F [auth B]	453	Escherichia 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 P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
Find proteins for Q8S307 (Arabidopsis thaliana) Explore Q8S307  Go to UniProtKB:  Q8S307
UniProt Groups	Q8S307P0AEY0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	15	synthetic construct

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J, K, L	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	M [auth C], N [auth C], O [auth D], P [auth A], Q [auth A], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	I, J, K, L	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.244 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.701	α = 90
b = 92.603	β = 100.42
c = 111.967	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Nosaki, S., Miyakawa, T., Xu, Y., Nakamura, A., Hirabayashi, K., Tanokura, M.

Revision History  

• 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