8J48

Crystal structure of OY phytoplasma SAP05 in complex with AtGATA18

• PDB DOI: https://doi.org/10.2210/pdb8J48/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana, Onion yellows phytoplasma OY-M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-19 Released: 2024-02-28 
• Deposition Author(s): Dong, C., Yan, X., Yuan, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 

Literature

Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors

Yan, X., Yuan, X., Lv, J., Zhang, B., Huang, Y., Li, Q., Ma, J., Li, Y., Wang, X., Li, Y., Yu, Y., Liu, Q., Liu, T., Mi, W., Dong, C.

(2024) Nat Commun 15: 1170

• DOI: https://doi.org/10.1038/s41467-024-45521-7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.04 kDa 
• Atom Count: 2,456 
• Modelled Residue Count: 276 
• Deposited Residue Count: 312 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GATA transcription factor 18	A [auth D], C [auth A]	52	Arabidopsis thaliana	Mutation(s): 0  Gene Names: GATA18
UniProt
Find proteins for Q8LC79 (Arabidopsis thaliana) Explore Q8LC79  Go to UniProtKB:  Q8LC79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sequence-variable mosaic (SVM) signal sequence domain-containing protein	B, D [auth C]	104	Onion yellows phytoplasma OY-M	Mutation(s): 0  Gene Names: PAM_518
UniProt
Find proteins for Q6YQ57 (Onion yellows phytoplasma (strain OY-M)) Explore Q6YQ57  Go to UniProtKB:  Q6YQ57

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth D], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.835	α = 90
b = 73.397	β = 107.22
c = 58.671	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Dong, C., Yan, X., Yuan, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31900865
National Natural Science Foundation of China (NSFC)	China	32271265
National Natural Science Foundation of China (NSFC)	China	32071193
National Natural Science Foundation of China (NSFC)	China	81874039

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Structure summary