7ODK | pdb_00007odk

Plant peptide hormone receptor H1

PDB DOI: https://doi.org/10.2210/pdb7ODK/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2021-04-29 Released: 2022-02-16
Deposition Author(s): Roman, A.O., Jimenez-Sandoval, P., Santiago, J.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.216 (Depositor), 0.226 (DCC)
R-Value Work:
0.204 (Depositor), 0.212 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 35169143 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-28558-4
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 142.98 kDa
Atom Count: 10,222
Modeled Residue Count: 1,174
Deposited Residue Count: 1,234
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-like protein kinase HSL1	A [auth AAA], B [auth BBB]	617	Arabidopsis thaliana	Mutation(s): 0 Gene Names: HSL1, At1g28440, F3M18.12 EC: 2.7.11.1
UniProt
Find proteins for Q9SGP2 (Arabidopsis thaliana) Explore Q9SGP2 Go to UniProtKB: Q9SGP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SGP2
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A [auth AAA] Focus chain B [auth BBB]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth AlA], J [auth BkB]	3		N-Glycosylation	Interactions Focus chain C [auth AlA] Focus chain J [auth BkB] Interactions & Density Focus chain C [auth AlA] Focus chain J [auth BkB]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth AmA], E [auth AnA], F [auth AoA], G [auth AqA], K [auth BmB], D [auth AmA], E [auth AnA], F [auth AoA], G [auth AqA], K [auth BmB], L [auth BoB], M [auth BpB], O [auth BvB], P [auth BwB]	2		N-Glycosylation	Interactions Focus chain D [auth AmA] Focus chain E [auth AnA] Focus chain F [auth AoA] Focus chain G [auth AqA] Focus chain K [auth BmB] Focus chain L [auth BoB] Focus chain M [auth BpB] Focus chain O [auth BvB] Focus chain P [auth BwB] Interactions & Density Focus chain D [auth AmA] Focus chain E [auth AnA] Focus chain F [auth AoA] Focus chain G [auth AqA] Focus chain K [auth BmB] Focus chain L [auth BoB] Focus chain M [auth BpB] Focus chain O [auth BvB] Focus chain P [auth BwB]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth AsA], N [auth BqB]	4		N-Glycosylation	Interactions Focus chain H [auth AsA] Focus chain N [auth BqB] Interactions & Density Focus chain H [auth AsA] Focus chain N [auth BqB]
Glycosylation Resources
GlyTouCan: G63564LA GlyCosmos: G63564LA GlyGen: G63564LA

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth AwA]	3		N-Glycosylation	Interactions Focus chain I [auth AwA] Interactions & Density Focus chain I [auth AwA]
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain RA [auth BBB] SDF format, chain QA [auth BBB] SDF format, chain PA [auth BBB] SDF format, chain DA [auth AAA] SDF format, chain CA [auth AAA] SDF format, chain BA [auth AAA] MOL2 format, chain RA [auth BBB] MOL2 format, chain QA [auth BBB] MOL2 format, chain PA [auth BBB] MOL2 format, chain DA [auth AAA] MOL2 format, chain CA [auth AAA] MOL2 format, chain BA [auth AAA] mmCIF format, chain RA [auth BBB] mmCIF format, chain QA [auth BBB] mmCIF format, chain PA [auth BBB] mmCIF format, chain DA [auth AAA] mmCIF format, chain CA [auth AAA] mmCIF format, chain BA [auth AAA]	BA [auth AAA] CA [auth AAA] DA [auth AAA] PA [auth BBB] QA [auth BBB] BA [auth AAA], CA [auth AAA], DA [auth AAA], PA [auth BBB], QA [auth BBB], RA [auth BBB]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth AAA] Focus chain CA [auth AAA] Focus chain DA [auth AAA] Focus chain PA [auth BBB] Focus chain QA [auth BBB] Focus chain RA [auth BBB] Interactions & Density Focus chain BA [auth AAA] Focus chain CA [auth AAA] Focus chain DA [auth AAA] Focus chain PA [auth BBB] Focus chain QA [auth BBB] Focus chain RA [auth BBB]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain SA [auth BBB] SDF format, chain EA [auth AAA] MOL2 format, chain SA [auth BBB] MOL2 format, chain EA [auth AAA] mmCIF format, chain SA [auth BBB] mmCIF format, chain EA [auth AAA]	EA [auth AAA], SA [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth AAA] Focus chain SA [auth BBB] Interactions & Density Focus chain EA [auth AAA] Focus chain SA [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain KA [auth BBB] SDF format, chain U [auth AAA] SDF format, chain Z [auth AAA] SDF format, chain Y [auth AAA] SDF format, chain X [auth AAA] SDF format, chain W [auth AAA] SDF format, chain V [auth AAA] SDF format, chain T [auth AAA] SDF format, chain S [auth AAA] SDF format, chain R [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain NA [auth BBB] SDF format, chain MA [auth BBB] SDF format, chain LA [auth BBB] SDF format, chain JA [auth BBB] SDF format, chain IA [auth BBB] SDF format, chain HA [auth BBB] SDF format, chain GA [auth BBB] SDF format, chain FA [auth BBB] SDF format, chain AA [auth AAA] MOL2 format, chain KA [auth BBB] MOL2 format, chain U [auth AAA] MOL2 format, chain Z [auth AAA] MOL2 format, chain Y [auth AAA] MOL2 format, chain X [auth AAA] MOL2 format, chain W [auth AAA] MOL2 format, chain V [auth AAA] MOL2 format, chain T [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain NA [auth BBB] MOL2 format, chain MA [auth BBB] MOL2 format, chain LA [auth BBB] MOL2 format, chain JA [auth BBB] MOL2 format, chain IA [auth BBB] MOL2 format, chain HA [auth BBB] MOL2 format, chain GA [auth BBB] MOL2 format, chain FA [auth BBB] MOL2 format, chain AA [auth AAA] mmCIF format, chain KA [auth BBB] mmCIF format, chain U [auth AAA] mmCIF format, chain Z [auth AAA] mmCIF format, chain Y [auth AAA] mmCIF format, chain X [auth AAA] mmCIF format, chain W [auth AAA] mmCIF format, chain V [auth AAA] mmCIF format, chain T [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain OA [auth BBB] mmCIF format, chain NA [auth BBB] mmCIF format, chain MA [auth BBB] mmCIF format, chain LA [auth BBB] mmCIF format, chain JA [auth BBB] mmCIF format, chain IA [auth BBB] mmCIF format, chain HA [auth BBB] mmCIF format, chain GA [auth BBB] mmCIF format, chain FA [auth BBB] mmCIF format, chain AA [auth AAA]	AA [auth AAA] FA [auth BBB] GA [auth BBB] HA [auth BBB] IA [auth BBB] AA [auth AAA], FA [auth BBB], GA [auth BBB], HA [auth BBB], IA [auth BBB], JA [auth BBB], KA [auth BBB], LA [auth BBB], MA [auth BBB], NA [auth BBB], OA [auth BBB], Q [auth AAA], R [auth AAA], S [auth AAA], T [auth AAA], U [auth AAA], V [auth AAA], W [auth AAA], X [auth AAA], Y [auth AAA], Z [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth AAA] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain MA [auth BBB] Focus chain NA [auth BBB] Focus chain OA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA] Interactions & Density Focus chain AA [auth AAA] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain MA [auth BBB] Focus chain NA [auth BBB] Focus chain OA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain TA [auth BBB] MOL2 format, chain TA [auth BBB] mmCIF format, chain TA [auth BBB]	TA [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain TA [auth BBB] Interactions & Density Focus chain TA [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.216 (Depositor), 0.226 (DCC)
R-Value Work: 0.204 (Depositor), 0.212 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.539	α = 99.178
b = 84.001	β = 113.727
c = 89.061	γ = 108.41

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Roman, A.O.

Jimenez-Sandoval, P.

Santiago, J.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_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
Version 1.3: 2024-11-20
Changes: Structure summary