Backbone-modified variant of zinc finger 2 from the transcription factor Sp1 DNA binding domain: Orn in the metal-binding turn

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2019-07-19 Released: 2020-06-24 
  • Deposition Author(s): Rao, S.R., Horne, W.S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Proteomimetic Zinc Finger Domains with Modified Metal-binding beta-Turns.

Rao, S.R.Horne, W.S.

(2020) Pept Sci (Hoboken) 112

  • DOI: https://doi.org/10.1002/pep2.24177
  • Primary Citation of Related Structures:  
    6PV0, 6PV1, 6PV2, 6PV3, 6UCO, 6UCP

  • PubMed Abstract: 

    The mimicry of protein tertiary folds by chains artificial in backbone chemical composition leads to proteomimetic analogues with potential utility as bioactive agents and as tools to shed light on biomacromolecule behavior. Notable successes toward such molecules have been achieved; however, as protein structural diversity is vast, design principles must be continually honed as they are applied to new prototype folding patterns. One specific structure where a gap remains in understanding how to effectively generate modified backbone analogues is the metal-binding β-turn found in zinc finger domains. Literature precedent suggests several factors that may act in concert, including the artificial moiety used to modify the turn, the sequence in which it is applied, and modifications present elsewhere in the domain. Here, we report efforts to gain insights into these issues and leverage these insights to construct a zinc finger mimetic with backbone modifications throughout its constituent secondary structures. We first conduct a systematic comparison of four turn mimetics in a common host sequence, quantifying relative efficacy for use in a metal-binding context. We go on to construct a proteomimetic zinc finger domain in which the helix, strands, and turn are simultaneously modified, resulting in a variant with 23% artificial residues, a tertiary fold indistinguishable from the prototype, and a folded stability comparable to the natural backbone on which the variant is based. Collectively, the results reported provide new insights into the effects of backbone modification on structure and stability of metal-binding domains and help inform the design of metalloprotein mimetics.

  • Organizational Affiliation

    Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor Sp131Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P08047 (Homo sapiens)
Explore P08047 
Go to UniProtKB:  P08047
GTEx:  ENSG00000185591 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08047
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
Query on NLE
Query on ORN
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107161

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2023-11-15
    Changes: Data collection