1PXE | pdb_00001pxe

Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1

• PDB DOI: https://doi.org/10.2210/pdb1PXE/pdb
• BMRB: 5901

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


• Deposited: 2003-07-03 Released: 2004-02-10 
• Deposition Author(s): Berkovits-Cymet, H.J., Amann, B.T., Berg, J.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 21 
• Selection Criteria: The submitted conformer models are those with the lowest energies. 

Literature

Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1 and Its Implications for DNA Binding.

Berkovits-Cymet, H.J., Amann, B.T., Berg, J.M.

(2004) Biochemistry 43: 898-903

• PubMed: 14744132 
• DOI: https://doi.org/10.1021/bi035159d
• Primary Citation Related Structures: 
  1PXE


• PubMed Abstract: 
  

  The structure of a CCHHC zinc-binding domain from neural zinc finger factor-1 (NZF-1) has been determined in solution though the use of NMR methods. This domain is a member of a family of domains that have the Cys-X(4)-Cys-X(4)-His-X(7)-His-X(5)-Cys consensus sequence. The structure determination reveals a novel fold based around a zinc(II) ion coordinated to three Cys residues and the second of the two conserved His residues. The other His residue is stacked between the metal-coordinated His residue and a relatively conserved aromatic residue. Analysis of His to Gln sequence variants reveals that both His residues are required for the formation of a well-defined structure, but neither is required for high-affinity metal binding at a tetrahedral site. The structure suggests that a two-domain protein fragment and a double-stranded DNA binding site may interact with a common two-fold axis relating the two domains and the two half-sites of the DNA-inverted repeat.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.2 kDa 
• Atom Count: 368 
• Modeled Residue Count: 48 
• Deposited Residue Count: 63 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
neural zinc finger transcription factor 1	A	63	Rattus norvegicus	Mutation(s): 0  Gene Names: NZF-1
UniProt
Find proteins for P70475 (Rattus norvegicus) Explore P70475  Go to UniProtKB:  P70475

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: 30 
• Conformers Submitted: 21 
• Selection Criteria: The submitted conformer models are those with the lowest energies. 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-10 
Deposition Author(s): Berkovits-Cymet, H.J., Amann, B.T., Berg, J.M.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2007-10-16
  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
• Version 1.4: 2022-12-21
  Changes: Database references
• Version 1.5: 2024-05-22
  Changes: Data collection