7R1O

p62-ZZ domain of the human sequestosome in complex with dusquetide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Dusquetide modulates innate immune response through binding to p62.

Zhang, Y.Towers, C.G.Singh, U.K.Liu, J.Hakansson, M.Logan, D.T.Donini, O.Kutateladze, T.G.

(2022) Structure 30: 1055

  • DOI: https://doi.org/10.1016/j.str.2022.05.003
  • Primary Citation of Related Structures:  
    7R1O

  • PubMed Abstract: 

    SQSTM1/p62 is an autophagic receptor that plays a major role in mediating stress and innate immune responses. Preclinical studies identified p62 as a target of the prototype innate defense regulator (IDR); however, the molecular mechanism of this process remains unclear. Here, we describe the structural basis and biological consequences of the interaction of p62 with the next generation of IDRs, dusquetide. Both electrostatic and hydrophobic contacts drive the formation of the complex between dusquetide and the ZZ domain of p62. We show that dusquetide penetrates the cell membrane and associates with p62 in vivo. Dusquetide binding modulates the p62-RIP1 complex, increases p38 phosphorylation, and enhances CEBP/B expression without activating autophagy. Our findings provide molecular details underlying the IDR action that may help in the development of new strategies to pharmacologically target p62.


  • Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA. Electronic address: yi.zhang26@case.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sequestosome-1A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
53Homo sapiensMutation(s): 0 
Gene Names: SQSTM1ORCAOSIL
UniProt & NIH Common Fund Data Resources
Find proteins for Q13501 (Homo sapiens)
Explore Q13501 
Go to UniProtKB:  Q13501
PHAROS:  Q13501
GTEx:  ENSG00000161011 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13501
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DusquetideE [auth EEE],
F [auth FFF]
5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth AAA]
I [auth BBB]
J [auth BBB]
K [auth CCC]
G [auth AAA],
H [auth AAA],
I [auth BBB],
J [auth BBB],
K [auth CCC],
L [auth CCC],
M [auth DDD],
N [auth DDD]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.07α = 90
b = 25.15β = 124.915
c = 77.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
XSCALEdata scaling
SHELXDEphasing
BUCCANEERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-08-17
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-06-19
    Changes: Data collection