5Y96

Crystal structure of ANXUR1 extracellular domain from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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This is version 2.1 of the entry. See complete history


Literature

Crystal structures of the extracellular domains of the CrRLK1L receptor-like kinases ANXUR1 and ANXUR2

Du, S.Qu, L.J.Xiao, J.

(2018) Protein Sci 27: 886-892

  • DOI: https://doi.org/10.1002/pro.3381
  • Primary Citation of Related Structures:  
    5Y92, 5Y96

  • PubMed Abstract: 

    Catharanthus roseus Receptor-Like Kinase 1-like (CrRLK1L) proteins contain two tandem malectin-like modules in their extracellular domains (ECDs) and function in diverse signaling pathways in plants. Malectin is a carbohydrate-binding protein in animals and recognizes a number of diglucosides; however, it remains unclear how the two malectin-like domains in the CrRLK1L proteins sense the ligand molecule. In this study, we reveal the crystal structures of the ECDs of ANXUR1 and ANXUR2, two CrRLK1L members in Arabidopsis thaliana that have critical functions in controlling pollen tube rupture during the fertilization process. We show that the two malectin-like domains in these proteins pack together to form a rigid architecture. Unlike animal malectin, these malectin-like domains lack residues involved in binding to the diglucosides, suggesting that they have a distinct ligand-binding mechanism. A cleft is observed between the two malectin-like domains, which might function as a potential ligand-binding pocket.


  • Organizational Affiliation

    The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase ANXUR1384Arabidopsis thalianaMutation(s): 0 
Gene Names: ANX1At3g04690F7O18.16
EC: 2.7.11.1
UniProt
Find proteins for Q9SR05 (Arabidopsis thaliana)
Explore Q9SR05 
Go to UniProtKB:  Q9SR05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SR05
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase ANXUR1383Arabidopsis thalianaMutation(s): 0 
Gene Names: ANX1At3g04690F7O18.16
EC: 2.7.11.1
UniProt
Find proteins for Q9SR05 (Arabidopsis thaliana)
Explore Q9SR05 
Go to UniProtKB:  Q9SR05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SR05
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.679α = 88.95
b = 68.74β = 75
c = 70.327γ = 72.18
Software Package:
Software NamePurpose
PHENIXrefinement
SOLVEphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary