1ZNM

A zinc finger with an artificial beta-turn, original sequence taken from the third zinc finger domain of the human transcriptional repressor protein YY1 (YING and YANG 1, a delta transcription factor), nmr, 34 structures


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 34 
  • Selection Criteria: NO NOE VIOLATIONS ABOVE 0.2 ANGSTROM AND 5 DEGREE DIHEDRAL ANGLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design, synthesis and structure of a zinc finger with an artificial beta-turn.

Viles, J.H.Patel, S.U.Mitchell, J.B.Moody, C.M.Justice, D.E.Uppenbrink, J.Doyle, P.M.Harris, C.J.Sadler, P.J.Thornton, J.M.

(1998) J Mol Biol 279: 973-986

  • DOI: https://doi.org/10.1006/jmbi.1998.1764
  • Primary Citation of Related Structures:  
    1ZNM

  • PubMed Abstract: 

    We have incorporated a bicyclic beta-turn mimetic (BTD; beta-turn dipeptide) into a zinc finger, creating a zinc finger with an artificial beta-turn. The designed peptide chelates zinc and has the same fold as the unmodified native zinc finger (finger 3 of the human YY1 protein). A combination of 1H NMR and structure calculations reveals that, in solution, this zinc finger has a fold similar to the known wild-type crystal structure and to other zinc fingers containing the consensus sequence X3-Cys-X4-Cys-X12-His-X3-His-X. The peptide was designed with BTD between the chelating cysteine residues, with BTD forming a type II' beta-turn linking the two strands of a distorted anti-parallel beta-sheet. The C-terminal portion of the peptide forms a helix with zinc co-ordinating histidine residues on successive turns of the helix. This work represents a step towards developing methods by which parts of a target protein may be replaced by peptide mimetics.


  • Organizational Affiliation

    Department of Chemistry, Birkbeck College, University of London, Gordon House, London, WC1H 0PP, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YY128N/AMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P25490 (Homo sapiens)
Explore P25490 
Go to UniProtKB:  P25490
PHAROS:  P25490
GTEx:  ENSG00000100811 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25490
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NVA
Query on NVA
A
L-PEPTIDE LINKINGC5 H11 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 34 
  • Selection Criteria: NO NOE VIOLATIONS ABOVE 0.2 ANGSTROM AND 5 DEGREE DIHEDRAL ANGLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-01
    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: 2017-11-29
    Changes: Derived calculations, Other