1NJ3 | pdb_00001nj3

Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4

• PDB DOI: https://doi.org/10.2210/pdb1NJ3/pdb
• BMRB: 5669

• Classification: PROTEIN BINDING
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-12-30 Released: 2003-04-22 
• Deposition Author(s): Wang, B., Alam, S.L., Meyer, H.H., Payne, M., Stemmler, T.L., Davis, D.R., Sundquist, W.I.

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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 

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 Biological Chem 278: 20225-20234

• PubMed: 12644454 
• DOI: https://doi.org/10.1074/jbc.M300459200
• Primary Citation Related Structures: 
  1NJ3


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Utah, Salt Lake City 84132, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.44 kDa 
• Atom Count: 230 
• Modeled Residue Count: 31 
• Deposited Residue Count: 31 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPL4	A	31	Rattus norvegicus	Mutation(s): 0  Gene Names: Npl4
UniProt
Find proteins for Q9ES54 (Rattus norvegicus) Explore Q9ES54  Go to UniProtKB:  Q9ES54

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Wang, B., Alam, S.L., Meyer, H.H., Payne, M., Stemmler, T.L., Davis, D.R., Sundquist, W.I.

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-22
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-01
  Changes: Data collection, Database references, Derived calculations