5IYX

Crystal structure of the Arabidopsis receptor kinase HAESA in complex with the peptide hormone IDA and the co-receptor SERK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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This is version 2.0 of the entry. See complete history


Literature

Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission.

Santiago, J.Brandt, B.Wildhagen, M.Hohmann, U.Hothorn, L.A.Butenko, M.A.Hothorn, M.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.15075
  • Primary Citation of Related Structures:  
    5IXO, 5IXQ, 5IXT, 5IYV, 5IYX

  • PubMed Abstract: 
  • Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs. Floral abscission is controlled by the leucine-rich repeat receptor kinase (LRR-RK) HAESA and the peptide hormone IDA. It is unknown how expression of IDA in the abscission zone leads to HAESA activation ...

    Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs. Floral abscission is controlled by the leucine-rich repeat receptor kinase (LRR-RK) HAESA and the peptide hormone IDA. It is unknown how expression of IDA in the abscission zone leads to HAESA activation. Here we show that IDA is sensed directly by the HAESA ectodomain. Crystal structures of HAESA in complex with IDA reveal a hormone binding pocket that accommodates an active dodecamer peptide. A central hydroxyproline residue anchors IDA to the receptor. The HAESA co-receptor SERK1, a positive regulator of the floral abscission pathway, allows for high-affinity sensing of the peptide hormone by binding to an Arg-His-Asn motif in IDA. This sequence pattern is conserved among diverse plant peptides, suggesting that plant peptide hormone receptors may share a common ligand binding mode and activation mechanism.


    Organizational Affiliation

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-like protein kinase 5658Arabidopsis thalianaMutation(s): 0 
Gene Names: RLK5HAEAt4g28490F21O9.180
EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for P47735 (Arabidopsis thaliana)
Explore P47735 
Go to UniProtKB:  P47735
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UniProt GroupP47735
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein IDA14Arabidopsis thalianaMutation(s): 1 
Gene Names: IDAAt1g68765F14K14
UniProt
Find proteins for Q8LAD7 (Arabidopsis thaliana)
Explore Q8LAD7 
Go to UniProtKB:  Q8LAD7
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UniProt GroupQ8LAD7
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Somatic embryogenesis receptor kinase 1201Arabidopsis thalianaMutation(s): 2 
Gene Names: SERK1At1g71830F14O23.21F14O23_24
EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94AG2 (Arabidopsis thaliana)
Explore Q94AG2 
Go to UniProtKB:  Q94AG2
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UniProt GroupQ94AG2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
L [auth C],
M [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
B
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.507α = 90
b = 100.456β = 90
c = 142.759γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary