5EPP

Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4.

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

(2016) Biochem J 473: 2863-2880

  • DOI: https://doi.org/10.1042/BCJ20160237
  • Primary Citation of Related Structures:  
    5EPP

  • PubMed Abstract: 

    RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N. Notably, the RF residues in VBM are involved in the interaction with p97N, showing a similar interaction pattern with that of FPR signature motif in the UBX domain, although the directionality is opposite. Comparison of VBM interaction with VIM of gp78, another α-helical motif that interacts with p97N, revealed that the helix direction is inversed. Nevertheless, the conserved arginine residues in both motifs participate in the majority of the interface via extensive hydrogen bonds and ionic interactions with p97N. We identified novel VBM-binding mode to p97N that involves a combination of two types of p97-cofactor specificities observed in the UBX and VIM interactions. This highlights the induced fit model of p97N interdomain cleft upon cofactor binding to form stable p97-cofactor complexes. Our mutational and biochemical analyses in defining the specific interaction between VBM and p97N have elucidated the importance of the highly conserved VBM, applicable to other VBM-containing proteins. We also showed that RHBDL4, ubiquitins, and p97 co-operate for efficient substrate dislocation.


  • Organizational Affiliation

    School of Life Science, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase184Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
PHAROS:  P55072
GTEx:  ENSG00000165280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rhomboid-related protein 415Homo sapiensMutation(s): 0 
EC: 3.4.21.105
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEB9 (Homo sapiens)
Explore Q8TEB9 
Go to UniProtKB:  Q8TEB9
PHAROS:  Q8TEB9
GTEx:  ENSG00000144468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TEB9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.999α = 90
b = 96.999β = 90
c = 50.902γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data processing
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description