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 
  • R-Value Observed: 0.191 

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
  • Primary Citation of Related Structures:  
    5GLF

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPaseACEG184Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
NIH Common Fund Data Resources
PHAROS  P55072
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Derlin-1BDFH12Homo sapiensMutation(s): 0 
Gene Names: DERL1DER1UNQ243/PRO276
Find proteins for Q9BUN8 (Homo sapiens)
Explore Q9BUN8 
Go to UniProtKB:  Q9BUN8
NIH Common Fund Data Resources
PHAROS  Q9BUN8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.802α = 90
b = 74.402β = 90
c = 222.114γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
MOLREPdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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