5GLF

Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the interaction of human p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease.

Lim, J.J.Lee, Y.Yoon, S.Y.Ly, T.T.Kang, J.Y.Youn, H.S.An, J.Y.Lee, J.G.Park, K.R.Kim, T.G.Yang, J.K.Jun, Y.Eom, S.H.

(2016) FEBS Lett. 590: 4402-4413

  • DOI: 10.1002/1873-3468.12447

  • PubMed Abstract: 
  • The interaction of the rhomboid pseudoprotease Derlin-1 and p97 is crucial for the retrotranslocation of polyubiquitinated substrates in the endoplasmic reticulum-associated degradation pathway. We report a 2.25 Å resolution structure of the p97 N-te ...

    The interaction of the rhomboid pseudoprotease Derlin-1 and p97 is crucial for the retrotranslocation of polyubiquitinated substrates in the endoplasmic reticulum-associated degradation pathway. We report a 2.25 Å resolution structure of the p97 N-terminal domain (p97N) in complex with the Derlin-1 SHP motif. Remarkably, the SHP motif adopts a short, antiparallel β-strand that interacts with the β-sheet of p97N-a site distinct from that to which most p97 adaptor proteins bind. Mutational and biochemical analyses contributed to defining the specific interaction, demonstrating the importance of a highly conserved binding pocket on p97N and a signature motif on SHP. Our findings may also provide insights into the interactions between other SHP-containing proteins and p97N.


    Organizational Affiliation

    Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Korea.,School of Life Science, Gwangju Institute of Science and Technology (GIST), Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea.,Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPase
A, C, E, G
184Homo 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
Derlin-1
B, D, F, H
12Homo sapiensMutation(s): 0 
Gene Names: DERL1 (DER1)
Find proteins for Q9BUN8 (Homo sapiens)
Go to Gene View: DERL1
Go to UniProtKB:  Q9BUN8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.802α = 90.00
b = 74.402β = 90.00
c = 222.114γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOLREPdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references, Derived calculations