3VHT

Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.

Suzuki, N.Rohaim, A.Kato, R.Dikic, I.Wakatsuki, S.Kawasaki, M.

(2016) Febs J. --: --

  • DOI: 10.1111/febs.13734
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating β-β-α fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here, we report the crystal structure of the UBZ domain of Y-family DNA polymeras ...

    The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating β-β-α fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here, we report the crystal structure of the UBZ domain of Y-family DNA polymerase (pol) η and the crystal structure of the complex between the UBZ domain of Werner helicase-interacting protein 1 (WRNIP1) and ubiquitin, crystallized using the GFP fusion technique. In contrast to the pol η UBZ, which has been proposed to bind ubiquitin via its C-terminal α-helix, ubiquitin binds to a novel surface of WRNIP1 UBZ composed of the first β-strand and the C-terminal α-helix. In addition, we report the structure of the tandem UBZ domains of Tax1-binding protein 1 (TAX1BP1) and show that the second UBZ of TAX1BP1 binds ubiquitin, presumably in a manner similar to that of WRNIP1 UBZ. We propose that UBZ domains can be divided into at least two different types in terms of the ubiquitin-binding surfaces: the pol η type and the WRNIP1 type.


    Organizational Affiliation

    Cardiovascular Research institute, the University of California at San Francisco, CA, USA.,Department of Structural Biology, School of Medicine, Stanford University, CA, USA.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.,Departement of Biophysics, Faculty of Science, Cairo University, Giza, Egypt.,Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany.,Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.,Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
235Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein,ATPase WRNIP1
B
273Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: WRNIP1 (WHIP), GFP
EC: 3.6.1.3
Find proteins for Q96S55 (Homo sapiens)
Go to Gene View: WRNIP1
Go to UniProtKB:  Q96S55
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
C
76Mus musculusMutation(s): 0 
Gene Names: Rps27a (Uba80, Ubcep1)
Find proteins for P62983 (Mus musculus)
Go to UniProtKB:  P62983
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A, B
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 88.950α = 90.00
b = 143.692β = 90.00
c = 106.864γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
MOLREPphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2017-06-28
    Type: Database references, Source and taxonomy, Structure summary