5FWI | pdb_00005fwi

structure of usp7 catalytic domain and three ubl-domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.267 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of Usp7 Catalytic Domain and Three Ubl-Domains Reveals a Connector Alpha-Helix with Regulatory Role.

Kim, R.Q.Van Dijk, W.J.Sixma, T.K.

(2016) J Struct Biol 195: 11

  • DOI: https://doi.org/10.1016/j.jsb.2016.05.005
  • Primary Citation Related Structures: 
    5FWI

  • PubMed Abstract: 

    Ubiquitin conjugation is an important signal in cellular pathways, changing the fate of a target protein, by degradation, relocalisation or complex formation. These signals are balanced by deubiquitinating enzymes (DUBs), which antagonize ubiquitination of specific protein substrates. Because ubiquitination pathways are critically important, DUB activity is often carefully controlled. USP7 is a highly abundant DUB with numerous targets that plays complex roles in diverse pathways, including DNA regulation, p53 stress response and endosomal protein recycling. Full-length USP7 switches between an inactive and an active state, tuned by the positioning of 5 Ubl folds in the C-terminal HUBL domain. The active state requires interaction between the last two Ubls (USP7(45)) and the catalytic domain (USP7(CD)), and this can be promoted by allosteric interaction from the first 3 Ubl domains of USP7 (USP7(123)) interacting with GMPS. Here we study the transition between USP7 states. We provide a crystal structure of USP7(CD123) and show that CD and Ubl123 are connected via an extended charged alpha helix. Mutational analysis is used to determine whether the charge and rigidity of this 'connector helix' are important for full USP7 activity.


  • Organizational Affiliation
    • Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 78.8 kDa 
  • Atom Count: 5,352 
  • Modeled Residue Count: 662 
  • Deposited Residue Count: 680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7A [auth C]680Homo sapiensMutation(s): 0 
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
GTEx:  ENSG00000187555 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.267 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.183α = 90
b = 195.04β = 90
c = 219.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description