3OJ3

Crystal structure of the A20 ZnF4 and ubiquitin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-KB Signaling

Bosanac, I.Wertz, I.E.Pan, B.Yu, C.Kusam, S.Lam, C.Phu, L.Phung, Q.Maurer, B.Arnott, D.Kirkpatrick, D.S.Dixit, V.M.Hymowitz, S.G.

(2010) Mol.Cell 40: 548-557

  • DOI: 10.1016/j.molcel.2010.10.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inactivating mutations in the ubiquitin (Ub) editing protein A20 promote persistent nuclear factor (NF)-κB signaling and are genetically linked to inflammatory diseases and hematologic cancers. A20 tightly regulates NF-κB signaling by acting as an Ub ...

    Inactivating mutations in the ubiquitin (Ub) editing protein A20 promote persistent nuclear factor (NF)-κB signaling and are genetically linked to inflammatory diseases and hematologic cancers. A20 tightly regulates NF-κB signaling by acting as an Ub editor, removing K63-linked Ub chains and mediating addition of Ub chains that target substrates for degradation. However, a precise molecular understanding of how A20 modulates this pathway remains elusive. Here, using structural analysis, domain mapping, and functional assays, we show that A20 zinc finger 4 (ZnF4) does not directly interact with E2 enzymes but instead can bind mono-Ub and K63-linked poly-Ub. Mutations to the A20 ZnF4 Ub-binding surface result in decreased A20-mediated ubiquitination and impaired regulation of NF-κB signaling. Collectively, our studies illuminate the mechanistically distinct but biologically interdependent activities of the A20 ZnF and ovarian tumor (OTU) domains that are inherent to the Ub editing process and, ultimately, to regulation of NF-κB signaling.


    Organizational Affiliation

    Department of Structural Biology, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, B, C, D, E, F, G, H
79Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor alpha-induced protein 3
I, J, K, L, M, N, O, P
49Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3 (OTUD7C)
EC: 2.3.2.-, 3.4.19.12
Find proteins for P21580 (Homo sapiens)
Go to Gene View: TNFAIP3
Go to UniProtKB:  P21580
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
I, J, K, L, M, N, O, P
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.830α = 90.00
b = 170.030β = 90.10
c = 66.239γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PHENIXrefinement
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-09
    Type: Source and taxonomy
  • Version 1.3: 2018-01-24
    Type: Structure summary