9IMU | pdb_00009imu

The complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR-PikD

• PDB DOI: https://doi.org/10.2210/pdb9IMU/pdb

• Classification: PLANT PROTEIN
• Organism(s): Oryza sativa, Pyricularia oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-04 Released: 2025-07-09 
• Deposition Author(s): Zhang, X., Liu, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

The complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR-PikD

Zhang, X., Liu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.48 kDa 
• Atom Count: 1,248 
• Modeled Residue Count: 156 
• Deposited Residue Count: 156 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance protein RGA5	A	75	Oryza sativa	Mutation(s): 0  Gene Names: RGA5
UniProt
Find proteins for F7J0N2 (Oryza sativa subsp. japonica) Explore F7J0N2  Go to UniProtKB:  F7J0N2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AVR-Pik protein	B [auth C]	81	Pyricularia oryzae	Mutation(s): 0  Gene Names: AVR-Pik, AvrPik, Pikm, Pikp
UniProt
Find proteins for A0AA97NPM3 (Pyricularia oryzae (strain Y34)) Explore A0AA97NPM3  Go to UniProtKB:  A0AA97NPM3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.41	α = 90
b = 66.41	β = 90
c = 84.446	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Zhang, X., Liu, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release