6SAK

Structure of the OTULINcat C129A - SNX27 PDZ domain complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Regulation of the endosomal SNX27-retromer by OTULIN.

Stangl, A.Elliott, P.R.Pinto-Fernandez, A.Bonham, S.Harrison, L.Schaub, A.Kutzner, K.Keusekotten, K.Pfluger, P.T.El Oualid, F.Kessler, B.M.Komander, D.Krappmann, D.

(2019) Nat Commun 10: 4320-4320

  • DOI: 10.1038/s41467-019-12309-z
  • Primary Citation of Related Structures:  
    6SAK

  • PubMed Abstract: 
  • OTULIN (OTU Deubiquitinase With Linear Linkage Specificity) specifically hydrolyzes methionine1 (Met1)-linked ubiquitin chains conjugated by LUBAC (linear ubiquitin chain assembly complex). Here we report on the mass spectrometric identification of the OTULIN interactor SNX27 (sorting nexin 27), an adaptor of the endosomal retromer complex responsible for protein recycling to the cell surface ...

    OTULIN (OTU Deubiquitinase With Linear Linkage Specificity) specifically hydrolyzes methionine1 (Met1)-linked ubiquitin chains conjugated by LUBAC (linear ubiquitin chain assembly complex). Here we report on the mass spectrometric identification of the OTULIN interactor SNX27 (sorting nexin 27), an adaptor of the endosomal retromer complex responsible for protein recycling to the cell surface. The C-terminal PDZ-binding motif (PDZbm) in OTULIN associates with the cargo-binding site in the PDZ domain of SNX27. By solving the structure of the OTU domain in complex with the PDZ domain, we demonstrate that a second interface contributes to the selective, high affinity interaction of OTULIN and SNX27. SNX27 does not affect OTULIN catalytic activity, OTULIN-LUBAC binding or Met1-linked ubiquitin chain homeostasis. However, via association, OTULIN antagonizes SNX27-dependent cargo loading, binding of SNX27 to the VPS26A-retromer subunit and endosome-to-plasma membrane trafficking. Thus, we define an additional, non-catalytic function of OTULIN in the regulation of SNX27-retromer assembly and recycling to the cell surface.


    Organizational Affiliation

    Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany. daniel.krappmann@helmholtz-muenchen.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin thioesterase otulinA, B275Homo sapiensMutation(s): 1 
Gene Names: OTULINFAM105B
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BN8 (Homo sapiens)
Explore Q96BN8 
Go to UniProtKB:  Q96BN8
PHAROS:  Q96BN8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin-27C, D96Homo sapiensMutation(s): 0 
Gene Names: SNX27KIAA0488My014
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L92 (Homo sapiens)
Explore Q96L92 
Go to UniProtKB:  Q96L92
PHAROS:  Q96L92
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , M [auth B] , N [auth B] , O [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.645α = 65.132
b = 62.912β = 85.976
c = 72.017γ = 85.38
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom724804

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release