5ZD4

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.

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

Starting Model: experimental
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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

PubMed: 30287951 Search on PubMed
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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q8S307P0AEY0
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPTPCPAPCPAPCPGPTPGPTPGPAPAP*A)-3')	C [auth G], D [auth H], G [auth E], H [auth F]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	M [auth C] N [auth C] O [auth D] P [auth A] Q [auth A] 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		Interactions Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

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

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 = 102.701	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

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Entry History

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

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