5B6C

Structural Details of Ufd1 binding to p97


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation

Le, L.T.M.Kang, W.Kim, J.Y.Le, O.T.T.Lee, S.Y.Yang, J.K.

(2016) PLoS ONE 11: e0163394-e0163394

  • DOI: 10.1371/journal.pone.0163394

  • PubMed Abstract: 
  • The hexameric ATPase p97 has been implicated in diverse cellular processes through interactions with many different adaptor proteins at its N-terminal domain. Among these, the Ufd1-Npl4 heterodimer is a major adaptor, and the p97-Ufd1-Npl4 complex pl ...

    The hexameric ATPase p97 has been implicated in diverse cellular processes through interactions with many different adaptor proteins at its N-terminal domain. Among these, the Ufd1-Npl4 heterodimer is a major adaptor, and the p97-Ufd1-Npl4 complex plays an essential role in endoplasmic reticulum-associated degradation (ERAD), acting as a segregase that translocates the ubiquitinated client protein from the ER membrane into the cytosol for proteasomal degradation. We determined the crystal structure of the complex of the N-terminal domain of p97 and the SHP box of Ufd1 at a resolution of 1.55 Å. The 11-residue-long SHP box of Ufd1 binds at the far-most side of the Nc lobe of the p97 N domain primarily through hydrophobic interactions, such that F225, F228, N233 and L235 of the SHP box contact hydrophobic residues on the surface of the p97 Nc lobe. Mutating these key interface residues abolished the interactions in two different binding experiments, isothermal titration calorimetry and co-immunoprecipitation. Furthermore, cycloheximide chase assays showed that these same mutations caused accumulation of tyrosinase-C89R, a well-known ERAD substrate, thus implying decreased rate of protein degradation due to their defects in ERAD function. Together, these results provide structural and biochemical insights into the interaction between p97 N domain and Ufd1 SHP box.


    Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 156-743, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPase
A
174Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to Gene View: VCP
Go to UniProtKB:  P55072
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Ubiquitin fusion degradation protein 1 homolog
B
11Homo sapiensMutation(s): 0 
Gene Names: UFD1 (UFD1L)
Find proteins for Q92890 (Homo sapiens)
Go to Gene View: UFD1
Go to UniProtKB:  Q92890
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 107.270α = 90.00
b = 107.270β = 90.00
c = 44.040γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-05-26 
  • Released Date: 2017-01-04 
  • Deposition Author(s): Le, L.T.M., Yang, J.K.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic OfNRF-2014R1A2A2A01006834

Revision History 

  • Version 1.0: 2017-01-04
    Type: Initial release