5Y92

Crystal structure of ANXUR2 extracellular domain from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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This is version 2.0 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 ANXUR2387Arabidopsis thalianaMutation(s): 0 
Gene Names: ANX2At5g28680F4I4.60
EC: 2.7.11.1
UniProt
Find proteins for Q3E8W4 (Arabidopsis thaliana)
Explore Q3E8W4 
Go to UniProtKB:  Q3E8W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E8W4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.189α = 90
b = 103.189β = 90
c = 121.738γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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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