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)

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
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This is version 1.0 of the entry. See complete history.

Literature

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

Zhang, X., Liu, J.

To be published.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F7J0N2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AA97NPM3
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-07-09
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.