5JTV

USP7CD-UBL45 in complex with Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.312 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation.

Rouge, L.Bainbridge, T.W.Kwok, M.Tong, R.Di Lello, P.Wertz, I.E.Maurer, T.Ernst, J.A.Murray, J.

(2016) Structure 24: 1335-1345

  • DOI: 10.1016/j.str.2016.05.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The deubiquitinating enzyme USP7 has a pivotal role in regulating the stability of proteins involved in fundamental cellular processes of normal biology and disease. Despite the importance of USP7, the mechanisms underlying substrate recognition and ...

    The deubiquitinating enzyme USP7 has a pivotal role in regulating the stability of proteins involved in fundamental cellular processes of normal biology and disease. Despite the importance of USP7, the mechanisms underlying substrate recognition and catalytic activation are poorly understood. Here we present structural, biochemical, and biophysical analyses elucidating the molecular mechanism by which the C-terminal 19 amino acids of USP7 (residues 1084-1102) enhance the ubiquitin cleavage activity of the deubiquitinase (DUB) domain. Our data demonstrate that the C-terminal peptide binds the activation cleft in the catalytic domain and stabilizes the catalytically competent conformation of USP7. Additional structures of longer fragments of USP7, as well as solution studies, provide insight into full-length USP7, the role of the UBL domains, and demonstrate that both substrate recognition and deubiquitinase activity are highly regulated by the catalytic and noncatalytic domains of USP7, a feature that could be essential for the proper function of multi-domain DUBs.


    Organizational Affiliation

    Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA.,Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA. Electronic address: murray.jeremy@gene.com.,Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA.,Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA; Denali Therapeutics, South San Francisco, CA 94080, USA.,Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA; Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA. Electronic address: ernst.james@gene.com.,Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, C, E, G
594Homo sapiensMutation(s): 0 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, D, F, H
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.312 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.611α = 90.00
b = 115.520β = 90.00
c = 257.822γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release