3VHT

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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:  
    3WUP, 4Z4K, 4Z4M, 3VHS, 3VHT

  • 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 polymerase (p ...

    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: 

    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent protein A233Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
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Go to UniProtKB:  P42212
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent protein,ATPase WRNIP1 B271Aequorea victoria, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: GFP, WRNIP1, WHIP
EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
Find proteins for Q96S55 (Homo sapiens)
Explore Q96S55 
Go to UniProtKB:  Q96S55
NIH Common Fund Data Resources
PHAROS:  Q96S55
GTEx:  ENSG00000124535
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin C76Mus musculusMutation(s): 0 
Gene Names: Rps27a, Uba80, Ubcep1
Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2		AL-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.95α = 90
b = 143.692β = 90
c = 106.864γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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