7XWD

Apo-AtPRT6 UBR box

• PDB DOI: https://doi.org/10.2210/pdb7XWD/pdb

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


• Deposited: 2022-05-26 Released: 2023-05-31 
• Deposition Author(s): Kim, L., Song, H.K.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Structural analyses of plant PRT6-UBR box for Cys-Arg/N-degron pathway and insights into the plant submergence resistance

Kim, L., Lin, C.C., Lin, T.J., Cao, Y.C., Chen, M.C., Chou, M.Y., Lin, W.H., Kim, M., Wu, J.L., Shih, M.C., Song, H.K., Ho, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 7.8 kDa 
• Atom Count: 528 
• Modelled Residue Count: 70 
• Deposited Residue Count: 70 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase PRT6	A	70	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60 EC: 2.3.2.27
UniProt
Find proteins for F4KCC2 (Arabidopsis thaliana) Explore F4KCC2  Go to UniProtKB:  F4KCC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.165	α = 90
b = 87.165	β = 90
c = 74.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Kim, L., Song, H.K.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A2C3008285
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021M3A9I4030068
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1A6A1A10045235

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary