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), 0.280 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
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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), 0.280 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.230 (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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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