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: 10.1006/jmbi.1998.1764

  • 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 (finge ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YY1
A
28Homo sapiensMutation(s): 0 
Gene Names: YY1 (INO80S)
Find proteins for P25490 (Homo sapiens)
Go to Gene View: YY1
Go to UniProtKB:  P25490
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 
  • Olderado: 1ZNM Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other