Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 65.48 kDa 
• Atom Count: 3139 
• Residue Count: 414 
• Unique protein chains: 1

4KC9

Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism

• DOI: 10.2210/pdb4KC9/pdb

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


• Deposited: 2013-04-24 Released: 2013-05-29 
• Deposition Author(s): Duda, D.M., Olszewski, J.L., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.270 
• R-Value Observed: 0.274 

Literature

Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism.

Duda, D.M., Olszewski, J.L., Schuermann, J.P., Kurinov, I., Miller, D.J., Nourse, A., Alpi, A.F., Schulman, B.A.

(2013) Structure 21: 1030-1041

• PubMed: 23707686 
• DOI: 10.1016/j.str.2013.04.019
• Primary Citation of Related Structures:  
  4KC9, 4KBL


• PubMed Abstract: 
  

A distinct mechanism for ubiquitin (Ub) ligation has recently been proposed for the RING1-IBR-RING2 (RBR) family of E3s: an N-terminal RING1 domain recruits a thioester-linked intermediate complex between Ub and the E2 UbcH7, and a structurally distinct C-terminal RING2 domain displays a catalytic cysteine required for Ub ligation. To obtain insights into RBR E3s, we determined the crystal structure of the human homolog of Ariadne (HHARI), which reveals the individual RING1, IBR, and RING2 domains embedded in superdomains involving sequences specific to the Ariadne RBR subfamily. The central IBR is flanked on one side by RING1, which is exposed and binds UbcH7. On the other side, a C-terminal autoinhibitory "Ariadne domain" masks the RING2 active site. Insights into RBR E3 mechanisms are provided by structure-based mutations that indicate distinct steps of relief from autoinhibition, Ub transfer from E2 to HHARI, and ligation from the HHARI cysteine to a terminal acceptor.

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Organizational Affiliation: 

Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase ARIH1	A	559	Homo sapiens	Mutation(s): 0  Gene Names: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
Find proteins for Q9Y4X5 (Homo sapiens) Explore Q9Y4X5  Go to UniProtKB:  Q9Y4X5
NIH Common Fund Data Resources
PHAROS:  Q9Y4X5 GTEx:  ENSG00000166233

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.270 
• R-Value Observed: 0.274 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.126	α = 90
b = 96.126	β = 90
c = 151.329	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-24 
• Released Date: 2013-05-29 
Deposition Author(s): Duda, D.M., Olszewski, J.L., Schulman, B.A.

Revision History 

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references