9VBD | pdb_00009vbd

Cryo-EM structure of CARD1 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb9VBD/pdb
• EM Map EMD-64920: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana, Escherichia coli K-12
• Expression System: Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2025-06-04 Released: 2026-04-08 
• Deposition Author(s): Fukuda, Y., Ishihama, N., Laohavisit, A.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A copper-dependent redox-based hydrogen peroxide perception in plants.

Ishihama, N., Fukuda, Y., Shirano, Y., Fujimoto, K.J., Takizawa, K., Hiroyama, R., Ito, H., Nishimura, M., Yanai, T., Inoue, T., Shirasu, K., Laohavisit, A.

(2026) Nat Commun 17

• PubMed: 42151134 
• DOI: https://doi.org/10.1038/s41467-026-72573-8
• Primary Citation Related Structures: 
  9VBD, 9VBV


• PubMed Abstract: 
  

  Redox-related molecules, such as quinones and reactive oxygen species (ROS), are important signaling molecules for all living organisms. A plant-specific leucine-rich repeat receptor-like kinase (LRR-RLK) CANNOT RESPOND TO DMBQ 1 (CARD1), also known as HYDROGEN-PEROXIDE-INDUCED Ca ²⁺ INCREASES (HPCA1), perceives both quinones and ROS, but the mechanism by which it distinguishes between these two types of signals remains unclear. Here, we determine the structure of the CARD1 ectodomain and uncover its unique features. Structural studies, coupled with genetics and biochemical analysis, demonstrate that previously identified unique cysteine residues are not essential for signal perception in CARD1. Interestingly, CARD1 harbors a copper ion on the surface of the ectodomain via histidine-coordination that is crucial for hydrogen peroxide signaling. Our work reports a unique copper-dependent redox perception in plants and provides insight into interactions between receptors and non-peptide stimuli during perception.

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Organizational Affiliation: 
• RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
Graduate School of Pharmaceutical Sciences, The University of Osaka, Suita, Japan.
Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), The University of Osaka, Suita, Japan.
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.
THERS Technical Center, Nagoya University, Nagoya, Japan.
Center for Infectious Disease Education and Research (CiDER), The University of Osaka, Suita, Japan.
Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo, Japan.
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 101.31 kDa 
• Atom Count: 4,243 
• Modeled Residue Count: 521 
• Deposited Residue Count: 893 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein	A	893	Arabidopsis thaliana, Escherichia coli K-12 This entity is chimeric	Mutation(s): 0  Gene Names: HPCA1, At5g49760, K2I5, malE, b4034, JW3994 EC: 2.7.11.1
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q8GZ99 (Arabidopsis thaliana) Explore Q8GZ99  Go to UniProtKB:  Q8GZ99
UniProt Groups	Q8GZ99P0AEX9
Glycosylation
Glycosylation Sites: 8

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G40894EI GlyCosmos: G40894EI GlyGen: G40894EI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU (Subject of Investigation/LOI)	J [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.21.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-08 
Deposition Author(s): Fukuda, Y., Ishihama, N., Laohavisit, A.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2026-04-08
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Data collection, Database references