Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.26 kDa 
• Atom Count: 2247 
• Modelled Residue Count: 275 
• Deposited Residue Count: 276 
• Unique protein chains: 2

5DFL

Crystal structure of Ube2K~Ubiquitin conjugate

• PDB DOI: 10.2210/pdb5DFL/pdb

• Classification: LIGASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-27 Released: 2015-12-02 
• Deposition Author(s): Middleton, A.J., Day, C.L.
• Funding Organization(s): Marsden Fund, Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K.

Middleton, A.J., Day, C.L.

(2015) Sci Rep 5: 16793-16793

• PubMed: 26592444 
• DOI: 10.1038/srep16793
• Primary Citation of Related Structures:  
  5DFL


• PubMed Abstract: 
  

The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.

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Organizational Affiliation: 

Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A [auth B]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 K	B [auth A]	200	Homo sapiens	Mutation(s): 3  Gene Names: UBE2K, HIP2, LIG EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61086 (Homo sapiens) Explore P61086  Go to UniProtKB:  P61086
PHAROS:  P61086 GTEx:  ENSG00000078140

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.324	α = 90
b = 37.557	β = 90.43
c = 61.001	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-27 
• Released Date: 2015-12-02 
Deposition Author(s): Middleton, A.J., Day, C.L.

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Funding Organization	Location	Grant Number
Marsden Fund, Royal Society of New Zealand	New Zealand	--

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references