6KYW | pdb_00006kyw

S8-mSRK-S8-SP11 complex

• PDB DOI: https://doi.org/10.2210/pdb6KYW/pdb

• Classification: PLANT PROTEIN
• Organism(s): Brassica rapa
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-09-20 Released: 2020-09-16 
• Deposition Author(s): Murase, K., Hakoshima, T., Mori, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Mechanism of self/nonself-discrimination in Brassica self-incompatibility.

Murase, K., Moriwaki, Y., Mori, T., Liu, X., Masaka, C., Takada, Y., Maesaki, R., Mishima, M., Fujii, S., Hirano, Y., Kawabe, Z., Nagata, K., Terada, T., Suzuki, G., Watanabe, M., Shimizu, K., Hakoshima, T., Takayama, S.

(2020) Nat Commun 11: 4916-4916

• PubMed: 33004803 
• DOI: https://doi.org/10.1038/s41467-020-18698-w
• Primary Citation Related Structures: 
  6KYW


• PubMed Abstract: 
  

  Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (S receptor kinase) and pollen determinant SP11 (S-locus Protein 11, also named SCR) from the S-locus. Although the structure of the B. rapa S ₉ -SRK ectodomain (eSRK) and S ₉ -SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in Brassica SI by determining the S ₈ -eSRK-S ₈ -SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK-SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK-SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in Brassica SI.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan. [e-mail].
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan. [e-mail].
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan.
Graduate School of Science, Tokyo Metropolitan University, Tokyo, 192-0397, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582, Japan.
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192, Japan. [e-mail].
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 112.62 kDa 
• Atom Count: 7,006 
• Modeled Residue Count: 867 
• Deposited Residue Count: 978 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor protein kinase SRK8	A, B	443	Brassica rapa	Mutation(s): 12  EC: 2.7.11.1
UniProt
Find proteins for Q39276 (Brassica campestris) Explore Q39276  Go to UniProtKB:  Q39276
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S locus protein 11	C, D	46	Brassica rapa	Mutation(s): 0
UniProt
Find proteins for Q9SE17 (Brassica campestris) Explore Q9SE17  Go to UniProtKB:  Q9SE17

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.562	α = 90
b = 143.562	β = 90
c = 194.401	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Murase, K., Hakoshima, T., Mori, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	16H06380
Japan Society for the Promotion of Science	Japan	15K18683

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references
• Version 1.2: 2020-10-21
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary