3I3T | pdb_00003i3t

Crystal structure of covalent ubiquitin-USP21 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.218 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3I3T

This is version 1.3 of the entry. See complete history

Literature

A strategy for modulation of enzymes in the ubiquitin system.

Ernst, A.Avvakumov, G.Tong, J.Fan, Y.Zhao, Y.Alberts, P.Persaud, A.Walker, J.R.Neculai, A.M.Neculai, D.Vorobyov, A.Garg, P.Beatty, L.Chan, P.K.Juang, Y.C.Landry, M.C.Yeh, C.Zeqiraj, E.Karamboulas, K.Allali-Hassani, A.Vedadi, M.Tyers, M.Moffat, J.Sicheri, F.Pelletier, L.Durocher, D.Raught, B.Rotin, D.Yang, J.Moran, M.F.Dhe-Paganon, S.Sidhu, S.S.

(2013) Science 339: 590-595

  • DOI: https://doi.org/10.1126/science.1230161
  • Primary Citation Related Structures: 
    3I3T, 3MTN, 3N3K, 3V6E, 4I6L

  • PubMed Abstract: 

    The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.


  • Organizational Affiliation
    • Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 194.94 kDa 
  • Atom Count: 12,456 
  • Modeled Residue Count: 1,527 
  • Deposited Residue Count: 1,720 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 21A,
B [auth C],
C [auth E],
D [auth G]
355Homo sapiensMutation(s): 0 
Gene Names: PP1490USP21USP23
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK80 (Homo sapiens)
Explore Q9UK80 
Go to UniProtKB:  Q9UK80
PHAROS:  Q9UK80
GTEx:  ENSG00000143258 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK80
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UbiquitinE [auth B],
F [auth D],
G [auth F],
H
75Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA52UBA80UBBUBCUBCEP1UBCEP2UBQ
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
J [auth C],
K [auth E],
L [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NEH

Query on NEH



Download:Ideal Coordinates CCD File
M [auth B],
N [auth D],
O [auth F],
P [auth H]
ETHANAMINE
C2 H7 N
QUSNBJAOOMFDIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.218 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.428α = 88.71
b = 83.663β = 75.73
c = 118.792γ = 85.11
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description