7OGO

Plant peptide hormone receptor H1I1S1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.234 

Starting Model: experimental
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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
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein IDA-LIKE 1C [auth CCC],
F [auth FFF]
14Arabidopsis thalianaMutation(s): 0 
Gene Names: IDL1At3g25655T5M7
UniProt
Find proteins for Q29PV4 (Arabidopsis thaliana)
Explore Q29PV4 
Go to UniProtKB:  Q29PV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ29PV4
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth AaA]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth AeA],
R [auth DkD]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I [auth AhA],
J [auth AkA],
K [auth AnA],
M [auth BaB],
N [auth BcB],
I [auth AhA],
J [auth AkA],
K [auth AnA],
M [auth BaB],
N [auth BcB],
O [auth DaD],
P [auth DeD],
Q [auth DgD],
U [auth EaE],
V [auth EeE]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth ArA],
T [auth DqD]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
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-glucopyranoseS [auth DnD]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth DDD]
BA [auth DDD]
CA [auth DDD]
DA [auth DDD]
EA [auth EEE]
AA [auth DDD],
BA [auth DDD],
CA [auth DDD],
DA [auth DDD],
EA [auth EEE],
FA [auth EEE],
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
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: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.735α = 90
b = 146.405β = 90
c = 169.645γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
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