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. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
235Aequorea victoriaGene 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
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 musculusGene 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