5GR8

Crystal structure of PEPR1-AtPEP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.587 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1

Tang, J.Han, Z.F.Sun, Y.D.Zhang, H.Q.Gong, X.Q.Chai, J.J.

(2015) Cell Res. 25: 110-120

  • DOI: 10.1038/cr.2014.161

  • PubMed Abstract: 
  • The endogenous peptides AtPep1-8 in Arabidopsis mature from the conserved C-terminal portions of their precursor proteins PROPEP1-8, respectively. The two homologous leucine-rich repeat-receptor kinases (LRR-RKs) PEPR1 and PEPR2 act as receptors of A ...

    The endogenous peptides AtPep1-8 in Arabidopsis mature from the conserved C-terminal portions of their precursor proteins PROPEP1-8, respectively. The two homologous leucine-rich repeat-receptor kinases (LRR-RKs) PEPR1 and PEPR2 act as receptors of AtPeps. AtPep binding leads to stable association of PEPR1,2 with the shared receptor LRR-RK BAK1, eliciting immune responses similar to those induced by pathogens. Here we report a crystal structure of the extracellular LRR domain of PEPR1 (PEPR1LRR) in complex with AtPep1. The structure reveals that AtPep1 adopts a fully extended conformation and binds to the inner surface of the superhelical PEPR1LRR. Biochemical assays showed that AtPep1 is capable of inducing PEPR1LRR-BAK1LRR heterodimerization. The conserved C-terminal portion of AtPep1 dominates AtPep1 binding to PEPR1LRR, with the last amino acid of AtPep1 Asn23 forming extensive interactions with PEPR1LRR. Deletion of the last residue of AtPep1 significantly compromised AtPep1 interaction with PEPR1LRR. Together, our data reveal a conserved structural mechanism of AtPep1 recognition by PEPR1, providing significant insight into prediction of recognition of other peptides by their cognate LRR-RKs.


    Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucine-rich repeat receptor-like protein kinase PEPR1
A, D
710Arabidopsis thalianaMutation(s): 0 
Gene Names: PEPR1
EC: 2.7.11.1
Find proteins for Q9SSL9 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SSL9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elicitor peptide 1
J, P
17Arabidopsis thalianaMutation(s): 0 
Gene Names: PEP1 (PROPEP1)
Find proteins for Q9LV87 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LV87
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.587 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.490α = 90.00
b = 96.967β = 110.79
c = 106.013γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-08-08 
  • Released Date: 2016-12-14 
  • Deposition Author(s): Chai, J.J., Tang, J.

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release