7EB9

The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


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Literature

Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-kappa B 1 (ABIN1) and M1-Linked Ubiquitins.

Hong, J.Y.Lin, S.C.Kuo, B.J.Lo, Y.C.

(2021) J Mol Biol 433: 167116-167116

  • DOI: 10.1016/j.jmb.2021.167116
  • Primary Citation of Related Structures:  
    7EAL, 7EAO, 7EB9

  • PubMed Abstract: 
  • Polyubiquitination is important in controlling NF-κB signaling. Excessive NF-κB activity has been linked to inflammatory disorders and autoimmune diseases, while ABIN1 could attenuate NF-κB activation to maintain immune homeostasis by utilizing UBAN to recognize linear (M1)-linked polyubiquitinated NF-κB activation mediators, including NEMO, IRAK1 and RIP1 ...

    Polyubiquitination is important in controlling NF-κB signaling. Excessive NF-κB activity has been linked to inflammatory disorders and autoimmune diseases, while ABIN1 could attenuate NF-κB activation to maintain immune homeostasis by utilizing UBAN to recognize linear (M1)-linked polyubiquitinated NF-κB activation mediators, including NEMO, IRAK1 and RIP1. PolyUb-mediated UBAN recruitment remains undetermined, since the recognition studies focused mostly on di-ubiquitin (diUb). Here we report three crystal structures of human ABIN1 UBAN (hABIN1 UBAN ) in complex with M1-linked diUb, triUb, and tetraUb, respectively. Notably, the hABIN1 UBAN :diUb structure reveals that a diUb randomly binds one of the Ub-binding sites of the hABIN1 UBAN dimer and leaves the other site vacant. Together with the ITC and gel-filtration analyses, we found that M1-triUb and M1-tetraUb adopt two unique conformations, instead of an elongated one, and they preferentially use the N-terminal two-Ub unit to bind the primary Ub-binding site of a hABIN1 UBAN dimer and the C-terminal two-Ub unit to bind the secondary Ub-binding site of another hABIN1 UBAN dimer. Especially, our results suggest that two ABIN1 UBAN dimers cooperatively bind two UBAN-binding units of a tetraUb or vice versa. Since the UBAN family members share a conserved diUb-binding mode, our results suggest that M1-polyUb modification allows multiple copies of the two-tandem Ub unit to simultaneously coordinate multiple and/or different binding partners to increase their local concentrations and to facilitate the formation of a large signaling complex. Our study provides a structural-functional glimpse of M1-polyUb as a multiple-molecule binding platform to exert its intrinsic structural plasticity in mediating cellular signaling.


    Organizational Affiliation

    Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan. Electronic address: gracelo@ncku.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tetra ubiquitinA304Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TNFAIP3-interacting protein 1B, C99Homo sapiensMutation(s): 0 
Gene Names: TNIP1KIAA0113NAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15025 (Homo sapiens)
Explore Q15025 
Go to UniProtKB:  Q15025
PHAROS:  Q15025
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.221 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.381α = 90
b = 53.777β = 90
c = 240.115γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-03-09 
  • Released Date: 2021-07-21 
  • Deposition Author(s): Lo, Y.C., Lin, S.C.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 107-2320-B-006 -062 -MY3

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release