1NJ3

Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.

Wang, B.Alam, S.L.Meyer, H.H.Payne, M.Stemmler, T.L.Davis, D.R.Sundquist, W.I.

(2003) J.Biol.Chem. 278: 20225-20234

  • DOI: 10.1074/jbc.M300459200

  • PubMed Abstract: 
  • Ubiquitylated proteins are directed into a large number of different cellular pathways through interactions with effector proteins that contain conserved ubiquitin binding motifs. Here, we report the solution structure and ubiquitin binding propertie ...

    Ubiquitylated proteins are directed into a large number of different cellular pathways through interactions with effector proteins that contain conserved ubiquitin binding motifs. Here, we report the solution structure and ubiquitin binding properties of one such motif, the Npl4 zinc finger or RanBP2/Nup358 zinc finger (NZF) domain. Npl4 NZF forms a compact module composed of four antiparallel beta-strands linked by three ordered loops. A single zinc ion is coordinated by four conserved cysteines from the first and third loops, which form two rubredoxin knuckles. Npl4 NZF binds specifically, but weakly, to free ubiquitin using a conserved 13TF14 dipeptide to interact with the "Ile-44" surface of ubiquitin. Our studies reveal the structure of this versatile class of protein binding domains and provide a means for identifying the subset of NZF domains likely to bind ubiquitin.


    Related Citations: 
    • Direct binding of ubiquitin conjugates by the mammalian p97 adapter complexes, p47 and ufd1-Npl4
      Meyer, H.H.,Wang, Y.,Warren, G.
      (2002) Embo J. 21: 5645
    • A complex of mammalian ufd1 and nlp4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport
      Meyer, H.H.,Shorter, J.G.,Pappin, D.,Warren, G.
      (2000) Embo J. 15: 2181


    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City 84132, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NPL4
A
31Rattus norvegicusGene Names: Nploc4 (Npl4)
Find proteins for Q9ES54 (Rattus norvegicus)
Go to UniProtKB:  Q9ES54
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 
  • Olderado: 1NJ3 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations