7VN5 | pdb_00007vn5

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

PDB DOI: https://doi.org/10.2210/pdb7VN5/pdb
NAKB: 7VN5

Classification: TRANSCRIPTION
Organism(s): Serratia sp. FS14, Arabidopsis thaliana, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-10-10 Released: 2022-12-07
Deposition Author(s): Nosaki, S., Tanokura, M., Miyakawa, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.244 (Depositor), 0.246 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

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

PubMed: 36522451 Search on PubMed
DOI: https://doi.org/10.1038/s41477-022-01289-6
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 214.22 kDa
Atom Count: 15,367
Modeled Residue Count: 1,806
Deposited Residue Count: 1,816
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1	A [auth C], B [auth D], E [auth A], F [auth B]	439	Serratia sp. FS14, Arabidopsis thaliana This entity is chimeric	Mutation(s): 8 Gene Names: malE, JW3994, BZR1, BIS2, At1g75080, F9E10_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q8S307 P0AEX9
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(TPTPTPTPCPAPCPGPTPGPAPAPAPAP*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	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I [auth K], J [auth L], K [auth M], L [auth N]	2		N/A	Interactions Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Interactions & Density Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N]
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 C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth A] SDF format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth A] MOL2 format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Q [auth D]	M [auth C] N [auth C] O [auth C] P [auth C] Q [auth D] M [auth C], N [auth C], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth A], V [auth A], W [auth A], X [auth B], Y [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 C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [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 [auth K], J [auth L], K [auth M], L [auth N]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Interactions & Density Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.244 (Depositor), 0.246 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.622	α = 90
b = 93.923	β = 100.646
c = 112.75	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-07

Deposition Author(s):

Nosaki, S.

Tanokura, M.

Miyakawa, T.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17H05835, 19H04855, 19K23658, 21H02114
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101077