6N6R

Crystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Recognition of M1-Linked Ubiquitin Chains by Native and Phosphorylated UBAN Domains.

Herhaus, L.van den Bedem, H.Tang, S.Maslennikov, I.Wakatsuki, S.Dikic, I.Rahighi, S.

(2019) J.Mol.Biol. 431: 3146-3156

  • DOI: 10.1016/j.jmb.2019.06.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although the Ub-binding domain in ABIN proteins and NEMO (UBAN) is highly conserved, UBAN-containing proteins exhibit different Ub-binding properties, resulting in their diverse biological roles. Post-translational modifications further control UBAN ...

    Although the Ub-binding domain in ABIN proteins and NEMO (UBAN) is highly conserved, UBAN-containing proteins exhibit different Ub-binding properties, resulting in their diverse biological roles. Post-translational modifications further control UBAN domain specificity for poly-Ub chains. However, precisely, how the UBAN domain structurally confers such functional diversity remains poorly understood. Here we report crystal structures of ABIN-1 alone and in complex with one or two M1-linked di-Ub chains. ABIN-1 UBAN forms a homo-dimer that provides two symmetrical Ub-binding sites on either side of the coiled-coil structure. Moreover, crystal structures of ABIN1 UBAN in complex with di-Ub chains reveal a concentration-dependency of UBAN/di-Ub binding stoichiometry. Analysis of UBAN/M1-linked di-Ub binding characteristics indicates that phosphorylated S473 in OPTN and its corresponding phospho-mimetic residue in ABIN-1 (E484) are essential for high affinity interactions with M1-linked Ub chains. Also, a phospho-mimetic mutation of A303 in NEMO, corresponding to S473 of OPTN, increases binding affinity for M1-linked Ub chains. These findings are in line with the diverse physiological roles of UBAN domains, as phosphorylation of OPTN UBAN is required to enhance its binding to Ub during mitophagy.


    Organizational Affiliation

    Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Stra├če 15, 60438 Frankfurt am Main, Germany. Electronic address: ivan.dikic@biochem2.de.,Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Therapeutic Sciences and Bioengineering, University of California, San Francisco, CA 94158, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Structural Molecular Biology, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan. Electronic address: soichi.wakatsuki@stanford.edu.,Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA. Electronic address: rahighi@chapman.edu.,Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, C
157Homo 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 1
B, D
70Mus musculusMutation(s): 0 
Gene Names: Tnip1 (Abin, Naf1)
Find proteins for Q9WUU8 (Mus musculus)
Go to UniProtKB:  Q9WUU8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.900α = 90.00
b = 88.180β = 90.00
c = 105.900γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references