4X57 | pdb_00004x57

Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex

• PDB DOI: https://doi.org/10.2210/pdb4X57/pdb

• Classification: ligase/protein binding
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-04 Released: 2016-01-20 
• Deposition Author(s): Korolev, S., Koroleva, O., Lu, X., Downes, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Models: experimental

Literature

Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold ProteinComplex

Korolev, S., Koroleva, O., Lu, X., Downes, B.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 70.27 kDa 
• Atom Count: 3,750 
• Modeled Residue Count: 482 
• Deposited Residue Count: 634 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 8	A, C	179	Arabidopsis thaliana	Mutation(s): 0  Gene Names: UBC8, UBC4A, At5g41700, MBK23.24 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P35131 (Arabidopsis thaliana) Explore P35131  Go to UniProtKB:  P35131

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-anchored ubiquitin-fold protein 3	B, D	138	Arabidopsis thaliana	Mutation(s): 0  Gene Names: MUB3, At4g24990, F13M23.130
UniProt
Find proteins for Q9SW27 (Arabidopsis thaliana) Explore Q9SW27  Go to UniProtKB:  Q9SW27

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth C], G [auth C], H [auth C], I [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.716	α = 90
b = 135.716	β = 90
c = 202.134	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Korolev, S., Koroleva, O., Lu, X., Downes, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM096279

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description