8DVC

Receptor ShHTL5 from Striga hermonthica in complex with strigolactone agonist GR24

PDB DOI: https://doi.org/10.2210/pdb8DVC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Striga hermonthica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-07-28 Released: 2023-06-14
Deposition Author(s): Arellano-Saab, A., Skarina, T., Yim, V., Savchenko, A., Stogios, P.J., McCourt, P.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Consejo Nacional de Ciencia y Tecnologia (CONACYT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.242
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of a hormone-bound Striga strigolactone receptor.

Arellano-Saab, A., Skarina, T., Xu, Z., McErlean, C.S.P., Savchenko, A., Lumba, S., Stogios, P.J., McCourt, P.

(2023) Nat Plants 9: 883-888

PubMed: 37264151 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41477-023-01423-y
Primary Citation of Related Structures:
8DVC

PubMed Abstract:
Strigolactones (SLs) regulate many aspects of plant development, but ambiguities remain about how this hormone is perceived because SL-complexed receptor structures do not exist. We find that when SL binds the Striga receptor, ShHTL5, a series of conformational changes relative to the unbound state occur, but these events are not sufficient for signalling. Ligand-complexed receptors, however, form internal tunnels that posit an explanation for how SL exits its receptor after hydrolysis.

Organizational Affiliation

Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.

Macromolecule Content

Total Structure Weight: 153.4 kDa
Atom Count: 10,882
Modelled Residue Count: 1,347
Deposited Residue Count: 1,355
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyposensitive to light 5	A, B, C, D, E	271	Striga hermonthica	Mutation(s): 1 Gene Names: ShHTL5
UniProt
Find proteins for A0A0M5I297 (Striga hermonthica) Explore A0A0M5I297 Go to UniProtKB: A0A0M5I297
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M5I297
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TZU (Subject of Investigation/LOI) Query on TZU Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain GA [auth E] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C]	AA [auth D], F [auth A], GA [auth E], O [auth B], U [auth C]	(3R,3aR,8bS)-3-({[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]oxy}methyl)-3,3a,4,8b-tetrahydro-2H-indeno[1,2-b]furan-2-one C₁₇ H₁₆ O₅ SBWWVZFWHGNNPM-LXTVHRRPSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain GA [auth E] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain GA [auth E] Focus chain O [auth B] Focus chain U [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C]	BA [auth D] CA [auth D] DA [auth D] G [auth A] H [auth A] BA [auth D], CA [auth D], DA [auth D], G [auth A], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], P [auth B], Q [auth B], R [auth B], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	JA [auth E] K [auth A] KA [auth E] L [auth A] S [auth B] JA [auth E], K [auth A], KA [auth E], L [auth A], S [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B]	EA [auth D] FA [auth D] LA [auth E] M [auth A] N [auth A] EA [auth D], FA [auth D], LA [auth E], M [auth A], N [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.242
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.269	α = 90
b = 352.967	β = 90
c = 124.988	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	06752
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	507992
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	00356
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	04298
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	--