7XED | pdb_00007xed

Crystal Structure of OsCIE1-Ubox and OsUBC8 complex

• PDB DOI: https://doi.org/10.2210/pdb7XED/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-30 Released: 2023-10-04 
• Deposition Author(s): Zhang, Y., Yu, C.Z.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.249 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.231 (Depositor) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Release of a ubiquitin brake activates OsCERK1-triggered immunity in rice.

Wang, G., Chen, X., Yu, C., Shi, X., Lan, W., Gao, C., Yang, J., Dai, H., Zhang, X., Zhang, H., Zhao, B., Xie, Q., Yu, N., He, Z., Zhang, Y., Wang, E.

(2024) Nature 629: 1158-1164

• PubMed: 38750355 
• DOI: https://doi.org/10.1038/s41586-024-07418-9
• Primary Citation Related Structures: 
  7XED, 8HPB, 8HQB


• PubMed Abstract: 
  

  Plant pattern-recognition receptors perceive microorganism-associated molecular patterns to activate immune signalling ^1,2 . Activation of the pattern-recognition receptor kinase CERK1 is essential for immunity, but tight inhibition of receptor kinases in the absence of pathogen is crucial to prevent autoimmunity ^3,4 . Here we find that the U-box ubiquitin E3 ligase OsCIE1 acts as a molecular brake to inhibit OsCERK1 in rice. During homeostasis, OsCIE1 ubiquitinates OsCERK1, reducing its kinase activity. In the presence of the microorganism-associated molecular pattern chitin, active OsCERK1 phosphorylates OsCIE1 and blocks its E3 ligase activity, thus releasing the brake and promoting immunity. Phosphorylation of a serine within the U-box of OsCIE1 prevents its interaction with E2 ubiquitin-conjugating enzymes and serves as a phosphorylation switch. This phosphorylation site is conserved in E3 ligases from plants to animals. Our work identifies a ligand-released brake that enables dynamic immune regulation.

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Organizational Affiliation: 
• National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
The New Cornerstone Science Laboratory, Shenzhen, China.
University of the Chinese Academy of Sciences, Beijing, China.
National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China.
School of Life Science, Shanghai Normal University, Shanghai, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, Shanghai Tech University, Shanghai, China. [e-mail].
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. [e-mail].
The New Cornerstone Science Laboratory, Shenzhen, China. [e-mail].
School of Life Science and Technology, Shanghai Tech University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.98 kDa 
• Atom Count: 3,467 
• Modeled Residue Count: 454 
• Deposited Residue Count: 460 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBC core domain-containing protein	A, C [auth B]	150	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: OsJ_21490 EC: 2.3.2.23
UniProt
Find proteins for A3BC59 (Oryza sativa subsp. japonica) Explore A3BC59  Go to UniProtKB:  A3BC59

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U-box domain-containing protein 12	B [auth C], D	80	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: PUB12, Os06g0102700, LOC_Os06g01304, OSJNBa0075G19.19-1 EC: 2.3.2.27
UniProt
Find proteins for Q5VRH9 (Oryza sativa subsp. japonica) Explore Q5VRH9  Go to UniProtKB:  Q5VRH9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.249 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.231 (Depositor) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.29	α = 90
b = 132.55	β = 90
c = 47.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Zhang, Y., Yu, C.Z.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	YSBR-011

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Database references
• Version 1.3: 2026-03-04
  Changes: Refinement description, Structure summary