5IFR

Structure of the stable UBE2D3-UbDha conjugate

• PDB DOI:  https://doi.org/10.2210/pdb5IFR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-26 Released: 2016-05-11 
• Deposition Author(s): Pruneda, J.N., Mulder, M.P.C., Witting, K., Ovaa, H., Komander, D.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.243 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes.

Mulder, M.P., Witting, K., Berlin, I., Pruneda, J.N., Wu, K.P., Chang, J.G., Merkx, R., Bialas, J., Groettrup, M., Vertegaal, A.C., Schulman, B.A., Komander, D., Neefjes, J., El Oualid, F., Ovaa, H.

(2016) Nat Chem Biol 12: 523-530

• PubMed: 27182664 
• DOI: https://doi.org/10.1038/nchembio.2084
• Primary Citation of Related Structures:  
  5IFR


• PubMed Abstract: 
  

Post-translational modifications of proteins with ubiquitin (Ub) and ubiquitin-like modifiers (Ubls), orchestrated by a cascade of specialized E1, E2 and E3 enzymes, control a wide range of cellular processes. To monitor catalysis along these complex reaction pathways, we developed a cascading activity-based probe, UbDha. Similarly to the native Ub, upon ATP-dependent activation by the E1, UbDha can travel downstream to the E2 (and subsequently E3) enzymes through sequential trans-thioesterifications. Unlike the native Ub, at each step along the cascade, UbDha has the option to react irreversibly with active site cysteine residues of target enzymes, thus enabling their detection. We show that our cascading probe 'hops' and 'traps' catalytically active Ub-modifying enzymes (but not their substrates) by a mechanism diversifiable to Ubls. Our founder methodology, amenable to structural studies, proteome-wide profiling and monitoring of enzymatic activity in living cells, presents novel and versatile tools to interrogate Ub and Ubl cascades.

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Organizational Affiliation: 

Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25.67 kDa 
• Atom Count: 1,854 
• Modelled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	A	151	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D3, UBC5C, UBCH5C EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
PHAROS:  P61077

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.243 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.125	α = 90
b = 52.271	β = 100.78
c = 53.624	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: 2016-05-11 
Deposition Author(s): Pruneda, J.N., Mulder, M.P.C., Witting, K., Ovaa, H., Komander, D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105192732

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2016-06-29
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.5: 2019-07-10
  Changes: Data collection