5Z7Z | pdb_00005z7z

Crystal structure of Striga hermonthica Dwarf14 (ShD14)

  • Classification: HYDROLASE
  • Organism(s): Striga hermonthica
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2018-01-30 Released: 2018-08-29 
  • Deposition Author(s): Xu, Y., Miyakawa, T., Nakamura, A., Tanokura, M.
  • Funding Organization(s): Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan, Core Research for Evolutional Science and Technology Program of Japan Science and Technology Agency, Grant-in-Aid for Scientific Research on Innovative Areas from the Japan Society for the Promotion of Science (JSPS), JSPS KAKENHI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5Z7Z

This is version 1.2 of the entry. See complete history

Literature

Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga.

Xu, Y.Miyakawa, T.Nosaki, S.Nakamura, A.Lyu, Y.Nakamura, H.Ohto, U.Ishida, H.Shimizu, T.Asami, T.Tanokura, M.

(2018) Nat Commun 9: 3947-3947

  • DOI: https://doi.org/10.1038/s41467-018-06452-2
  • Primary Citation Related Structures: 
    5Z7W, 5Z7X, 5Z7Y, 5Z7Z

  • PubMed Abstract: 

    HYPOSENSITIVE TO LIGHT (HTL) and DWARF14 (D14) mediate the perception of karrikin and strigolactone, which stimulates germination of the parasitic weed Striga. However, their role in parasitic seeds is poorly understood, and the basis for their differing responsiveness remains unclear. Here, we show that Striga hermonthica HTL proteins (ShHTLs) in 'conserved' and 'intermediate' clades are able to bind karrikin. The 'divergent' clade is able to hydrolyze strigolactone. Unexpectedly, we find that ShD14 is also capable of hydrolyzing strigolactone. Through comparative analysis of ShHTLs and ShD14 crystal structures, we provide insights into the basis for their selectivity. Moreover, we show that both ShD14 and divergent clade ShHTLs, but not conserved and intermediate clade ShHTLs, can interact with the putative downstream signaling component ShMAX2 in the presence of the synthetic strigolactone, rac-GR24. These findings provide insight into how strigolactone is perceived and how ligand specificity is determined.


  • Organizational Affiliation
    • Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content 

  • Total Structure Weight: 60.5 kDa 
  • Atom Count: 4,620 
  • Modeled Residue Count: 529 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dwarf 14
A, B
272Striga hermonthicaMutation(s): 0 
UniProt
Find proteins for A0A2U8XQ45 (Striga hermonthica)
Explore A0A2U8XQ45 
Go to UniProtKB:  A0A2U8XQ45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2U8XQ45
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.662α = 90
b = 70.316β = 94.03
c = 84.684γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology of JapanJapan--
Core Research for Evolutional Science and Technology Program of Japan Science and Technology AgencyJapan--
Grant-in-Aid for Scientific Research on Innovative Areas from the Japan Society for the Promotion of Science (JSPS)JapanJP17H05835
JSPS KAKENHIJapanJP15H05621

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description