7OGU

Plant peptide hormone receptor complex H1C9S1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.238 

wwPDB Validation   3D Report Full Report


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],
G [auth GGG],
J [auth JJJ]
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],
H [auth HHH],
K [auth KKK]
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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CLAVATA3/ESR (CLE)-related protein 9C [auth CCC],
F [auth FFF],
I [auth III],
L [auth LLL]
12Arabidopsis thalianaMutation(s): 0 
Gene Names: CLE9At1g26600T1K7.3
UniProt
Find proteins for Q9FZE4 (Arabidopsis thaliana)
Explore Q9FZE4 
Go to UniProtKB:  Q9FZE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FZE4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth EdE],
EA [auth GgG],
GA [auth GlG],
HA [auth GnG],
IA [auth HaH],
BA [auth EdE],
EA [auth GgG],
GA [auth GlG],
HA [auth GnG],
IA [auth HaH],
JA [auth JaJ],
KA [auth JcJ],
LA [auth JeJ],
M [auth AaA],
MA [auth JgJ],
NA [auth JkJ],
OA [auth KaK],
P [auth AlA],
R [auth AqA],
S [auth AsA],
V [auth DeD],
W [auth DgD],
Y [auth DmD]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth AcA],
O [auth AhA],
X [auth DiD]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 6
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-glucopyranoseQ [auth AnA]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 7
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-glucopyranoseAA [auth EaE],
CA [auth GaG],
DA [auth GdG],
T [auth BaB],
U [auth DaD]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseZ [auth DpD]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth GjG]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 
BB [auth GGG]
DB [auth HHH]
FB [auth JJJ]
GB [auth JJJ]
HB [auth JJJ]
BB [auth GGG],
DB [auth HHH],
FB [auth JJJ],
GB [auth JJJ],
HB [auth JJJ],
IB [auth JJJ],
QA [auth AAA],
TA [auth BBB],
UA [auth BBB],
WA [auth DDD],
XA [auth DDD],
ZA [auth EEE]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
PA [auth AAA]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth EEE]
CB [auth GGG]
EB [auth HHH]
JB [auth KKK]
RA [auth AAA]
AB [auth EEE],
CB [auth GGG],
EB [auth HHH],
JB [auth KKK],
RA [auth AAA],
SA [auth AAA],
VA [auth BBB],
YA [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],
I [auth III],
L [auth LLL]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.962α = 90
b = 169.894β = 96.744
c = 143.547γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building

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