7XPC

Complex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1

• PDB DOI: https://doi.org/10.2210/pdb7XPC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Solanum lycopersicum, Phytophthora infestans T30-4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-05-04 Released: 2023-06-07 
• Deposition Author(s): Hu, Q., Zhou, J., Yao, D., Xing, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.317 
• R-Value Work: 0.293 
• R-Value Observed: 0.296 

Literature

Chloroplast Protein GLYK Hijacked by Phytophthora Infestans Effector AVRvnt1 in Cytoplasm to Activate NLR

Hu, Q., Zhou, J., Yao, D., Xing, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96.73 kDa 
• Atom Count: 6,550 
• Modelled Residue Count: 816 
• Deposited Residue Count: 842 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glycerate-3-kinase (GLYK)	A, C	337	Solanum lycopersicum	Mutation(s): 6
UniProt
Find proteins for A0A3Q7FWS2 (Solanum lycopersicum) Explore A0A3Q7FWS2  Go to UniProtKB:  A0A3Q7FWS2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein Avr-vnt11	B, D	84	Phytophthora infestans T30-4	Mutation(s): 0  Gene Names: Avr-vnt1, PITG_16294
UniProt
Find proteins for D0NTY1 (Phytophthora infestans (strain T30-4)) Explore D0NTY1  Go to UniProtKB:  D0NTY1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.317 
• R-Value Work: 0.293 
• R-Value Observed: 0.296 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.285	α = 90
b = 131.285	β = 90
c = 121.968	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Hu, Q., Zhou, J., Yao, D., Xing, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release