Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.95 kDa 
• Atom Count: 314 
• Modelled Residue Count: 39 
• Deposited Residue Count: 42 
• Unique protein chains: 1

1FRE

XNF7 BBOX, DEVELOPMENTAL PROTEIN, PH 7.5, 30 C, WITH ZINC, NMR, 1 STRUCTURE

• PDB DOI: 10.2210/pdb1FRE/pdb

• Classification: ZINC-BINDING PROTEIN
• Organism(s): Xenopus laevis
• Mutation(s): No 


• Deposited: 1996-01-31 Released: 1997-02-12 
• Deposition Author(s): Borden, K.L.B., Freemont, P.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development.

Borden, K.L., Lally, J.M., Martin, S.R., O'Reilly, N.J., Etkin, L.D., Freemont, P.S.

(1995) EMBO J 14: 5947-5956

• PubMed: 8846787 
• Primary Citation of Related Structures:  
  1FRE


• PubMed Abstract: 
  

Xenopus nuclear factor XNF7, a maternally expressed protein, functions in patterning of the embryo. XNF7 contains a number of defined protein domains implicated in the regulation of some developmental processes. Among these is a tripartite motif comprising a zinc-binding RING finger and B-box domain next to a predicted alpha-helical coiled-coil domain. Interestingly, this motif is found in a variety of protein including several proto-oncoproteins. Here we describe the solution structure of the XNF7 B-box zinc-binding domain determined at physiological pH by 1H NMR methods. The B-box structure represents the first three-dimensional structure of this new motif and comprises a monomer have two beta-strands, two helical turns and three extended loop regions packed in a novel topology. The r.m.s. deviation for the best 18 structures is 1.15 A for backbone atoms and 1.94 A for all atoms. Structure calculations and biochemical data shows one zinc atom ligated in a Cys2-His2 tetrahedral arrangement. We have used mutant peptides to determine the metal ligation scheme which surprisingly shows that not all of the seven conserved cysteines/histidines in the B-box motif are involved in metal ligation. The B-box structure is not similar in tertiary fold to any other known zinc-binding motif.

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Related Citations: 

• The Ring Finger. A Novel Protein Sequence Motif Related to the Zinc Finger
  Freemont, P.S.
  (1993) Ann N Y Acad Sci 684: 174

• The Cloning and Characterization of a Maternally Expressed Novel Zinc Finger Nuclear Phosphoprotein (Xnf7) in Xenopus Laevis
  Reddy, B.A., Kloc, M., Etkin, L.
  (1991) Dev Biol 148: 107

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Organizational Affiliation: 

Laboratory of Molecular Structure, National Institute for Medical Research, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR FACTOR XNF7	A	42	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for Q92021 (Xenopus laevis) Explore Q92021  Go to UniProtKB:  Q92021

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 Submitted: 1 
• OLDERADO: 1FRE Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-01-31 
• Released Date: 1997-02-12 
Deposition Author(s): Borden, K.L.B., Freemont, P.S.

Revision History  

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Other