7ODV

Plant peptide hormone receptor complex H1LS1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.255 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

HSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides.

Roman, A.O.Jimenez-Sandoval, P.Augustin, S.Broyart, C.Hothorn, L.A.Santiago, J.

(2022) Nat Commun 13: 876-876

  • DOI: https://doi.org/10.1038/s41467-022-28558-4
  • Primary Citation of Related Structures:  
    7ODK, 7ODV, 7OGO, 7OGQ, 7OGU, 7OGZ

  • PubMed Abstract: 

    The membrane receptor kinases HAESA and HSL2 recognize a family of IDA/IDL signaling peptides to control cell separation processes in different plant organs. The homologous HSL1 has been reported to regulate epidermal cell patterning by interacting with a different class of signaling peptides from the CLE family. Here we demonstrate that HSL1 binds IDA/IDL peptides with high, and CLE peptides with lower affinity, respectively. Ligand sensing capability and receptor activation of HSL1 require a SERK co-receptor kinase. Crystal structures with IDA/IDLs or with CLE9 reveal that HSL1-SERK1 complex recognizes the entire IDA/IDL signaling peptide, while only parts of CLE9 are bound to the receptor. In contrast, the receptor kinase BAM1 interacts with the entire CLE9 peptide with high affinity and specificity. Furthermore, the receptor tandem BAM1/BAM2 regulates epidermal cell division homeostasis. Consequently, HSL1-IDLs and BAM1/BAM2-CLEs independently regulate cell patterning in the leaf epidermal tissue.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase HSL1A [auth AAA],
D [auth DDD]
617Arabidopsis thalianaMutation(s): 0 
Gene Names: HSL1At1g28440F3M18.12
EC: 2.7.11.1
UniProt
Find proteins for Q9SGP2 (Arabidopsis thaliana)
Explore Q9SGP2 
Go to UniProtKB:  Q9SGP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SGP2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Somatic embryogenesis receptor kinase 1B [auth BBB],
E [auth EEE]
203Arabidopsis thalianaMutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94AG2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein IDAC [auth CCC],
F [auth FFF]
14Arabidopsis thalianaMutation(s): 0 
Gene Names: IDAAt1g68765F14K14
UniProt
Find proteins for Q8LAD7 (Arabidopsis thaliana)
Explore Q8LAD7 
Go to UniProtKB:  Q8LAD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LAD7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
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-glucopyranoseG [auth AdA],
J [auth AmA],
R [auth DmD]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H [auth AhA],
I [auth AkA],
K [auth BaB],
L [auth BeB],
M [auth DbD],
H [auth AhA],
I [auth AkA],
K [auth BaB],
L [auth BeB],
M [auth DbD],
N [auth DdD],
O [auth DgD],
P [auth DiD],
Q [auth DkD],
T [auth EaE],
U [auth EcE]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseS [auth DqD]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth BBB]
DA [auth BBB]
EA [auth BBB]
GA [auth DDD]
HA [auth DDD]
CA [auth BBB],
DA [auth BBB],
EA [auth BBB],
GA [auth DDD],
HA [auth DDD],
IA [auth DDD],
MA [auth EEE],
V [auth AAA],
W [auth AAA],
X [auth AAA],
Y [auth AAA],
Z [auth AAA]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth AAA],
FA [auth BBB],
JA [auth DDD],
NA [auth EEE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth AAA],
KA [auth DDD],
LA [auth DDD]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
C [auth CCC],
F [auth FFF]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.332α = 90
b = 145.878β = 90
c = 169.539γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_173101

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description