9H24 | pdb_00009h24

Crystal structure of MtCERK1 extracellular domain

PDB DOI: https://doi.org/10.2210/pdb9H24/pdb

Classification: PLANT PROTEIN
Organism(s): Medicago truncatula
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-10-10 Released: 2025-07-16
Deposition Author(s): Hansen, S.B., Gysel, K., Andersen, K.R.
Funding Organization(s): The Carlsberg Foundation, Danish Council for Independent Research, Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.284 (Depositor), 0.289 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural basis for size-selective perception of chitin in plants

Gysel, K., Hansen, S.B., Ruebsam, H., Alsarraf, H.M.A.B., Madland, E., Cheng, J.X.J., Baadegaard, C., Poulsen, E.C., Vinther, M., Fort, S., Stougaard, J., Andersen, K.R.

To be published.

Macromolecule Content

Total Structure Weight: 23.91 kDa
Atom Count: 1,574
Modeled Residue Count: 195
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM receptor kinase K1B	A	210	Medicago truncatula	Mutation(s): 0 Gene Names: 11442199, MTR_3g080050, MtrunA17_Chr3g0119241 EC: 2.7.11.1
UniProt
Find proteins for G7J6P5 (Medicago truncatula) Explore G7J6P5 Go to UniProtKB: G7J6P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7J6P5
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.284 (Depositor), 0.289 (DCC)
R-Value Work: 0.231 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.669	α = 90
b = 70.669	β = 90
c = 95.205	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
The Carlsberg Foundation	Denmark	CF21-0139
Danish Council for Independent Research	Denmark	3103-00137B
Novo Nordisk Foundation	Denmark	NNF21OC0071300

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.