3A9K

Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Literature

Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3

Sato, Y.Yoshikawa, A.Yamashita, M.Yamagata, A.Fukai, S.

(2009) EMBO J 28: 3903-3909

  • DOI: 10.1038/emboj.2009.345
  • Primary Citation of Related Structures:  
    3A9J, 3A9K

  • PubMed Abstract: 
  • TAB2 and TAB3 activate the Jun N-terminal kinase and nuclear factor-kappaB pathways through the specific recognition of Lys 63-linked polyubiquitin chains by its Npl4 zinc-finger (NZF) domain. Here we report crystal structures of the TAB2 and TAB3 NZ ...

    TAB2 and TAB3 activate the Jun N-terminal kinase and nuclear factor-kappaB pathways through the specific recognition of Lys 63-linked polyubiquitin chains by its Npl4 zinc-finger (NZF) domain. Here we report crystal structures of the TAB2 and TAB3 NZF domains in complex with Lys 63-linked diubiquitin at 1.18 and 1.40 A resolutions, respectively. Both NZF domains bind to the distal ubiquitin through a conserved Thr-Phe dipeptide that has been shown to be important for the interaction of the NZF domain of Npl4 with monoubiquitin. In contrast, a surface specific to TAB2 and TAB3 binds the proximal ubiquitin. Both the distal and proximal binding sites of the TAB2 and TAB3 NZF domains recognize the Ile 44-centred hydrophobic patch on ubiquitin but do not interact with the Lys 63-linked isopeptide bond. Mutagenesis experiments show that both binding sites are required to enable binding of Lys 63-linked diubiquitin. We therefore propose a mechanism for the recognition of Lys 63-linked polyubiquitin chains by TAB2 and TAB3 NZF domains in which diubiquitin units are specifically recognized by a single NZF domain.


    Organizational Affiliation

    Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA76Mus musculusMutation(s): 1 
Gene Names: UbiquitinUbc
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB77Mus musculusMutation(s): 1 
Gene Names: UbiquitinUbc
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 7-interacting protein 3C34Mus musculusMutation(s): 0 
Gene Names: TAB3 (AMINO ACIDS 688 - 716)Tab3Kiaa4135Map3k7ip3
Find proteins for Q571K4 (Mus musculus)
Explore Q571K4 
Go to UniProtKB:  Q571K4
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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.9α = 90
b = 71.018β = 90
c = 71.562γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance