1S3S

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.

Dreveny, I.Kondo, H.Uchiyama, K.Shaw, A.Zhang, X.Freemont, P.S.

(2004) EMBO J 23: 1030-1039

  • DOI: 10.1038/sj.emboj.7600139
  • Primary Citation of Related Structures:  
    1S3S

  • PubMed Abstract: 
  • The AAA ATPase p97/VCP is involved in many cellular events including ubiquitin-dependent processes and membrane fusion. In the latter, the p97 adaptor protein p47 is of central importance. In order to provide insight into the molecular basis of p97 adaptor binding, we have determined the crystal structure of p97 ND1 domains complexed with p47 C-terminal domain at 2 ...

    The AAA ATPase p97/VCP is involved in many cellular events including ubiquitin-dependent processes and membrane fusion. In the latter, the p97 adaptor protein p47 is of central importance. In order to provide insight into the molecular basis of p97 adaptor binding, we have determined the crystal structure of p97 ND1 domains complexed with p47 C-terminal domain at 2.9 A resolution. The structure reveals that the p47 ubiquitin regulatory X domain (UBX) domain interacts with the p97 N domain via a loop (S3/S4) that is highly conserved in UBX domains, but is absent in ubiquitin, which inserts into a hydrophobic pocket between the two p97 N subdomains. Deletion of this loop and point mutations in the loop significantly reduce p97 binding. This hydrophobic binding site is distinct from the predicted adaptor-binding site for the p97/VCP homologue N-ethylmaleimide sensitive factor (NSF). Together, our data suggest that UBX domains may act as general p97/VCP/CDC48 binding modules and that adaptor binding for NSF and p97 might involve different binding sites. We also propose a classification for ubiquitin-like domains containing or lacking a longer S3/S4 loop.


    Organizational Affiliation

    Centre for Structural Biology, Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin]A, B, C, D, E, F458Mus musculusMutation(s): 0 
Gene Names: Vcp
EC: 3.6.4.6
Find proteins for Q01853 (Mus musculus)
Explore Q01853 
Go to UniProtKB:  Q01853
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
p47 proteinG, H, I127Rattus norvegicusMutation(s): 0 
Gene Names: Nsfl1c
Find proteins for O35987 (Rattus norvegicus)
Explore O35987 
Go to UniProtKB:  O35987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.719α = 90
b = 157.719β = 90
c = 243.195γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance