6GRF

Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP8.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights into the evolution of DUF26-containing proteins in land plants.

Vaattovaara, A.Brandt, B.Rajaraman, S.Safronov, O.Veidenberg, A.Luklova, M.Kangasjarvi, J.Loytynoja, A.Hothorn, M.Salojarvi, J.Wrzaczek, M.

(2019) Commun Biol 2: 56-56

  • DOI: 10.1038/s42003-019-0306-9
  • Primary Citation of Related Structures:  
    6GRF, 6GRE

  • PubMed Abstract: 
  • Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins ...

    Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.


    Organizational Affiliation

    1Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine-rich repeat secretory protein 15A, B, C242Arabidopsis thalianaMutation(s): 0 
Gene Names: CRRSP15At3g60720T4C21_130PDLP8
UniProt
Find proteins for Q6NKQ9 (Arabidopsis thaliana)
Explore Q6NKQ9 
Go to UniProtKB:  Q6NKQ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.862α = 90
b = 143.862β = 90
c = 59.722γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_176237

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary