6FIH | pdb_00006fih

Crystal structure of the ANX2 ectodomain from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.183 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Crystal structures of two tandem malectin-like receptor kinases involved in plant reproduction.

Moussu, S.Augustin, S.Roman, A.O.Broyart, C.Santiago, J.

(2018) Acta Crystallogr D Struct Biol 74: 671-680

  • DOI: https://doi.org/10.1107/S205979831800774X
  • Primary Citation Related Structures: 
    6FIG, 6FIH

  • PubMed Abstract: 

    Complex cell-to-cell communication between the male pollen tube and the female reproductive organs is required for plant fertilization. A family of Catharanthus roseus receptor kinase 1-like (CrRLK1L) membrane receptors has been genetically implicated in this process. Here, crystal structures of the CrRLK1Ls ANXUR1 and ANXUR2 are reported at 1.48 and 1.1 Å resolution, respectively. The structures reveal a novel arrangement of two malectin-like domains connected by a short β-hairpin linker and stabilized by calcium ions. The canonical carbohydrate-interaction surfaces of related animal and bacterial carbohydrate-binding modules are not conserved in plant CrRLK1Ls. In line with this, the binding of chemically diverse oligosaccharides to ANXUR1 and HERCULES1 could not be detected. Instead, CrRLK1Ls have evolved a protein-protein interface between their malectin domains which forms a deep cleft lined by highly conserved aromatic and polar residues. Analysis of the glycosylation patterns of different CrRLK1Ls and their oligomeric states suggests that this cleft could resemble a binding site for a ligand required for receptor activation of CrRLK1Ls.


  • Organizational Affiliation
    • The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 47.56 kDa 
  • Atom Count: 3,574 
  • Modeled Residue Count: 379 
  • Deposited Residue Count: 412 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-like protein kinase ANXUR2412Arabidopsis 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
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.566α = 90
b = 41.766β = 117.37
c = 93.371γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2018-07-11 
  • Deposition Author(s): Santiago, J.

Funding OrganizationLocationGrant Number
European Research CouncilSwitzerlandWallWatchers 716358
Swiss National Science FoundationSwitzerland31003A_173101

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary