Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.02 kDa 
• Atom Count: 833 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 2

1Q5W

Ubiquitin Recognition by Npl4 Zinc-Fingers

• PDB DOI: 10.2210/pdb1Q5W/pdb
• BMRB: 5669

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


• Deposited: 2003-08-11 Released: 2004-03-30 
• Deposition Author(s): Alam, S.L., Sun, J., Payne, M., Welch, B.D., Blake, B.K., Davis, D.R., Meyer, H.H., Emr, S.D., Sundquist, W.I.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 

Literature

Ubiquitin interactions of NZF zinc fingers.

Alam, S.L., Sun, J., Payne, M., Welch, B.D., Blake, B.K., Davis, D.R., Meyer, H.H., Emr, S.D., Sundquist, W.I.

(2004) EMBO J 23: 1411-1421

• PubMed: 15029239 
• DOI: 10.1038/sj.emboj.7600114
• Primary Citation of Related Structures:  
  1Q5W


• PubMed Abstract: 
  

Ubiquitin (Ub) functions in many different biological pathways, where it typically interacts with proteins that contain modular Ub recognition domains. One such recognition domain is the Npl4 zinc finger (NZF), a compact zinc-binding module found in many proteins that function in Ub-dependent processes. We now report the solution structure of the NZF domain from Npl4 in complex with Ub. The structure reveals that three key NZF residues (13TF14/M25) surrounding the zinc coordination site bind the hydrophobic 'Ile44' surface of Ub. Mutations in the 13TF14/M25 motif inhibit Ub binding, and naturally occurring NZF domains that lack the motif do not bind Ub. However, substitution of the 13TF14/M25 motif into the nonbinding NZF domain from RanBP2 creates Ub-binding activity, demonstrating the versatility of the NZF scaffold. Finally, NZF mutations that inhibit Ub binding by the NZF domain of Vps36/ESCRT-II also inhibit sorting of ubiquitylated proteins into the yeast vacuole. Thus, the NZF is a versatile protein recognition domain that is used to bind ubiquitylated proteins during vacuolar protein sorting, and probably many other biological processes.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Biochemistry, University of Utah, Salt Lake City, UT, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
homolog of yeast nuclear protein localization 4	A	31	Rattus norvegicus	Mutation(s): 0  Gene Names: Npl4, Nploc4
UniProt
Find proteins for Q9ES54 (Rattus norvegicus) Explore Q9ES54  Go to UniProtKB:  Q9ES54

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: (UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR RPS27A), UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 
• OLDERADO: 1Q5W Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-11 
• Released Date: 2004-03-30 
Deposition Author(s): Alam, S.L., Sun, J., Payne, M., Welch, B.D., Blake, B.K., Davis, D.R., Meyer, H.H., Emr, S.D., Sundquist, W.I.

Revision History  

• Version 1.0: 2004-03-30
  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: 2022-03-02
  Changes: Data collection, Database references, Derived calculations