5KWN | pdb_00005kwn

The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from HY5

• PDB DOI: https://doi.org/10.2210/pdb5KWN/pdb

• Classification: Ligase/Peptide
• Organism(s): Arabidopsis thaliana, Arabidopsis
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-07-18 Released: 2017-07-26 
• Deposition Author(s): Uljon, S., Blacklow, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The COP1 WD domain in complex with HY5 peptide

Uljon, S., Blacklow, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.26 kDa 
• Atom Count: 2,877 
• Modeled Residue Count: 315 
• Deposited Residue Count: 355 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase COP1	A	336	Arabidopsis thaliana	Mutation(s): 0  Gene Names: COP1, At2g32950, T21L14.11 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for P43254 (Arabidopsis thaliana) Explore P43254  Go to UniProtKB:  P43254

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide 16-mer	B [auth U]	19	Arabidopsis	Mutation(s): 0
UniProt
Find proteins for O24646 (Arabidopsis thaliana) Explore O24646  Go to UniProtKB:  O24646

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.99	α = 90
b = 55.176	β = 90
c = 131.618	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-26 
Deposition Author(s): Uljon, S., Blacklow, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	K08CA166227

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description