3OJ4

Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.284 

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:  
    3OJ3, 3OJ4

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D1A, D153Homo sapiensMutation(s): 0 
Gene Names: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P51668 (Homo sapiens)
Explore P51668 
Go to UniProtKB:  P51668
NIH Common Fund Data Resources
PHAROS  P51668
GTEx  ENSG00000072401
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB, E79Homo sapiensMutation(s): 0 
Gene Names: UBB, UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor alpha-induced protein 3C, F49Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3, OTUD7C
EC: 2.3.2 (UniProt), 3.4.19.12 (UniProt)
Find proteins for P21580 (Homo sapiens)
Explore P21580 
Go to UniProtKB:  P21580
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PHAROS  P21580
GTEx  ENSG00000118503
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
C, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.284 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.646α = 90
b = 102.646β = 90
c = 112.686γ = 120
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary