5H07

TNIP2-Ub complex, C2 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.586 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Insights into Linear Tri-ubiquitin Recognition by A20-Binding Inhibitor of NF-kappa B, ABIN-2

Lin, S.M.Lin, S.C.Hong, J.Y.Su, T.W.Kuo, B.J.Chang, W.H.Tu, Y.F.Lo, Y.C.

(2017) Structure 25: 66-78

  • DOI: 10.1016/j.str.2016.11.005

  • PubMed Abstract: 
  • Recognition of linear polyubiquitin by specific ubiquitin-binding proteins plays an important role in mediating nuclear factor-κB (NF-κB) signaling. A20 binding proteins, ABINs, recognize linear polyubiquitin and A20 through UBAN and AHD1, respective ...

    Recognition of linear polyubiquitin by specific ubiquitin-binding proteins plays an important role in mediating nuclear factor-κB (NF-κB) signaling. A20 binding proteins, ABINs, recognize linear polyubiquitin and A20 through UBAN and AHD1, respectively, for the inhibition of NF-κB activation. Here we report the crystal structure of the AHD1-UBAN fragment of ABIN2 in complex with linear tri-ubiquitin, which reveals a 2:1 stoichiometry of the complex. Structural analyses together with mutagenesis, pull-down, and isothermal titration calorimetry assays show that the hABIN2:tri-ubiquitin interaction is mainly through the primary ubiquitin-binding site, and also through the secondary ubiquitin-binding site under a high local protein concentration. Surprisingly, three ubiquitin units could form a right-handed helical trimer to bridge two ABIN2 dimers. The residues around the M1-linkage are crucial for ABIN2 to recognize tri-ubiquitin. The tri-ubiquitin bridging two ABIN2 dimers model suggests a possible higher-order signaling complex assembled between M1-linked polyubiquitinated proteins, ubiquitin-binding proteins, and effector signaling proteins in signal transduction.


    Organizational Affiliation

    Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
A
228Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TNFAIP3-interacting protein 2
D, C
91Homo sapiensMutation(s): 0 
Gene Names: TNIP2 (ABIN2, FLIP1)
Find proteins for Q8NFZ5 (Homo sapiens)
Go to Gene View: TNIP2
Go to UniProtKB:  Q8NFZ5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.586 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.765α = 90.00
b = 80.972β = 114.28
c = 65.352γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-04 
  • Released Date: 2017-03-08 
  • Deposition Author(s): Lo, Y.C., Lin, S.C.

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwanNSC 101-2311-B-006-008-MY3
Ministry of Science and TechnologyTaiwanMOST 104-2320-B-006-033-MY3
Taiwan Protein ProjectTaiwanMOST 105-0210-01-12-01

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release