5TTE

Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI.

Yuan, L.Lv, Z.Atkison, J.H.Olsen, S.K.

(2017) Nat Commun 8: 211-211

  • DOI: 10.1038/s41467-017-00272-6

  • PubMed Abstract: 
  • RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligases function with Ub E2s through a RING/HECT hybrid mechanism to conjugate Ub to target proteins. Here, we report the crystal structure of the RBR E3, HHARI, in complex with a UbcH7 ~ Ub thioester mime ...

    RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligases function with Ub E2s through a RING/HECT hybrid mechanism to conjugate Ub to target proteins. Here, we report the crystal structure of the RBR E3, HHARI, in complex with a UbcH7 ~ Ub thioester mimetic which reveals the molecular basis for the specificity of this cognate E2/RBR E3 pair. The structure also reveals mechanistically important conformational changes in the RING1 and UBA-like domains of HHARI that accompany UbcH7 ~ Ub binding and provides a molecular basis by which HHARI recruits E2 ~ Ub in an 'open' conformation. In addition to optimally functioning with an E2 that solely performs transthiolation, our data suggests that HHARI prevents spurious discharge of Ub from E2 to lysine residues by: (1) harboring structural elements that block E2 ~ Ub from adopting a 'closed' conformation and (2) participating in contacts to ubiquitin that promote an open E2 ~ Ub conformation.HHARI is a RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligase. Here the authors present the crystal structure of HHARI with the UbcH7 ~ Ub thioester intermediate mimetic, which reveals that HHARI binds this E2 ~ Ub in an open conformation and explains the specificity of this cognate RBR E3/E2 pair.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase ARIH1
B
558Homo sapiensMutation(s): 0 
Gene Names: ARIH1 (ARI, MOP6, UBCH7BP)
EC: 2.3.2.31
Find proteins for Q9Y4X5 (Homo sapiens)
Go to Gene View: ARIH1
Go to UniProtKB:  Q9Y4X5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
E
167Homo sapiensMutation(s): 2 
Gene Names: UBE2L3 (UBCE7, UBCH7)
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Go to Gene View: UBE2L3
Go to UniProtKB:  P68036
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
F
86Triticum aestivumMutation(s): 7 
Find proteins for P69326 (Triticum aestivum)
Go to UniProtKB:  P69326
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.234α = 90.00
b = 154.234β = 90.00
c = 285.501γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115568-02

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references, Refinement description