3OJ4

Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB 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-conjugating enzyme E2 D1
A, D
153Homo sapiensMutation(s): 0 
Gene Names: UBE2D1 (SFT, UBC5A, UBCH5, UBCH5A)
EC: 2.3.2.23
Find proteins for P51668 (Homo sapiens)
Go to Gene View: UBE2D1
Go to UniProtKB:  P51668
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, E
79Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor alpha-induced protein 3
C, F
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 
C, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.280 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.646α = 90.00
b = 102.646β = 90.00
c = 112.686γ = 120.00
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


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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: 2018-01-24
    Type: Structure summary