5MN9

Crystal structure of MINDY-1 tMIU in complex with K48-diUb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains.

Kristariyanto, Y.A.Abdul Rehman, S.A.Weidlich, S.Knebel, A.Kulathu, Y.

(2017) EMBO Rep. 18: 392-402

  • DOI: 10.15252/embr.201643205

  • PubMed Abstract: 
  • The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub si ...

    The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.


    Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK ykulathu@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
A, B
76Bos taurusMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus)
Go to Gene View: RPS27A
Go to UniProtKB:  P62992
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase MINDY-1
C
44Homo sapiensMutation(s): 0 
Gene Names: MINDY1 (FAM63A, KIAA1390)
EC: 3.4.19.12
Find proteins for Q8N5J2 (Homo sapiens)
Go to Gene View: MINDY1
Go to UniProtKB:  Q8N5J2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 55.140α = 90.00
b = 55.140β = 90.00
c = 105.510γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UU_12016/6

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Data collection
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence