5GQR | pdb_00005gqr

Crystal structure of PXY-CLE41-SERK2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

SERK Family Receptor-like Kinases Function as Co-receptors with PXY for Plant Vascular Development

Zhang, H.Q.Lin, X.Y.Han, Z.F.Wang, J.Qu, L.J.Chai, J.J.

(2016) Mol Plant 9: 1406-1414

  • DOI: https://doi.org/10.1016/j.molp.2016.07.004
  • Primary Citation Related Structures: 
    5GQR

  • PubMed Abstract: 

    In Arabidopsis, the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) peptides play important roles in regulating proliferation and differentiation of plant-specific stem cells. Although receptors of CLEs are reported to be leucine-rich repeat receptor kinases, the mechanisms underlying CLE-induced receptor activation remain largely unknown. Here we show that SOMATIC EMBRYOGENESIS RECEPTOR KINASEs (SERKs) serve as co-receptors in CLE41/TDIF-PXY signaling to regulate plant vascular development. TDIF induces interaction of its receptor PXY with SERKs in vitro and in vivo. Furthermore, the serk1-1 serk2-1 bak1-5 mutant plants are less sensitive to TDIF, phenocopying the pxy mutant with a compromised promotion of procambial cell proliferation. Crystal structure of the PXY-TDIF-SERK2 complex reveals that the last amino acid of TDIF conserved among CLEs and other evolutionary-related peptides is important for the interaction between SERK2 and PXY. Taken together, our current study identifies SERKs as signaling components of the TDIF-PXY pathway and suggests a conserved activation mechanism of CLE receptors.


  • Organizational Affiliation
    • Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 88.19 kDa 
  • Atom Count: 6,160 
  • Modeled Residue Count: 790 
  • Deposited Residue Count: 795 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat receptor-like protein kinase TDRA [auth B]598Arabidopsis thalianaMutation(s): 0 
Gene Names: TDR
EC: 2.7.11.1
UniProt
Find proteins for Q9FII5 (Arabidopsis thaliana)
Explore Q9FII5 
Go to UniProtKB:  Q9FII5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FII5
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TDIFB [auth C]12ArabideaeMutation(s): 0 
UniProt
Find proteins for Q941C5 (Arabidopsis thaliana)
Explore Q941C5 
Go to UniProtKB:  Q941C5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941C5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Somatic embryogenesis receptor kinase 2C [auth K]185Arabidopsis thalianaMutation(s): 0 
Gene Names: SERK2
EC: 2.7.11.1
UniProt
Find proteins for Q9XIC7 (Arabidopsis thaliana)
Explore Q9XIC7 
Go to UniProtKB:  Q9XIC7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XIC7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.422α = 90
b = 162.422β = 90
c = 187.234γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary