8HMH

The closed state of RGLG2-VWA

• PDB DOI: https://doi.org/10.2210/pdb8HMH/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-03 Released: 2023-12-27 
• Deposition Author(s): Wang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.246 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

The regulation of RGLG2-VWA by Ca 2+ ions.

Zhang, M., Zhang, J., Liang, Y., Tian, S., Xie, S., Zhou, T., Wang, Q.

(2024) Biochim Biophys Acta Proteins Proteom 1872: 140966-140966

• PubMed: 37734561 
• DOI: https://doi.org/10.1016/j.bbapap.2023.140966
• Primary Citation of Related Structures:  
  8HMH


• PubMed Abstract: 
  

  RGLG2, an E3 ubiquitin ligase in Arabidopsis thaliana, affects hormone signaling and participates in drought regulation. Here, we determined two crystal structures of RGLG2 VWA domain, representing two conformations, open and closed, respectively. The two structures reveal that Ca ²⁺ ions are allosteric regulators of RGLG2-VWA, which adopts open state when NCBS1(Novel Calcium ions Binding Site 1) binds Ca ²⁺ ions and switches to closed state after Ca ²⁺ ions are removed. This mechanism of allosteric regulation is identical to RGLG1-VWA, but distinct from integrin α and β VWA domains. Therefore, our data provide a backdrop for understanding the role of the Ca ²⁺ ions in conformational change of VWA domain. In addition, we found that RGLG2 ^closed , corresponding to low affinity, can bind pseudo-ligand, which has never been observed in other VWA domains.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Binzhou Medical University, YanTai, ShanDong 264003, PR China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.95 kDa 
• Atom Count: 4,240 
• Modelled Residue Count: 537 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RGLG2	A [auth B], B [auth A]	307	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RGLG2, At5g14420, F18O22.210 EC: 2.3.2.27
UniProt
Find proteins for Q9LY87 (Arabidopsis thaliana) Explore Q9LY87  Go to UniProtKB:  Q9LY87

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth B], D [auth B], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B], B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.246 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.96	α = 90
b = 62.96	β = 90
c = 155.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Wang, Q.

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

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-01-03
  Changes: Database references