1U7J

Solution structure of a diiron protein model


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Analysis and Design of Turns in alpha-Helical Hairpins

Lahr, S.J.Engel, D.E.Stayrook, S.E.Maglio, O.North, B.Geremia, S.Lombardi, A.Degrado, W.F.

(2005) J.Mol.Biol. 346: 1441-1454

  • DOI: 10.1016/j.jmb.2004.12.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although the analysis and design of turns that connect the strands in antiparallel beta-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the ...

    Although the analysis and design of turns that connect the strands in antiparallel beta-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the structures and sequence preferences of two types of interhelical turns, each of which connects the two helices by a two-residue linker in an alphaL-beta conformation. Based on this analysis, it became apparent that the turn introduced into a designed four-helix bundle protein, DF1, did not occur within an optimal structural context. DF1 is a dimeric model for the diiron class of proteins. A longer loop with a beta-alphaR-beta conformation was inserted between two helices in the protein, and a sequence was chosen to stabilize its conformation. X-ray crystallography and NMR analysis of the protein showed the structure to be in excellent agreement with design.


    Related Citations: 
    • Preorganization of molecular binding sites in designed diiron proteins
      Maglio, O.,Nastri, F.,Pavone, V.,Lombardi, A.,DeGrado, W.F.
      (2003) Proc.Natl.Acad.Sci.USA 100: 3772
    • Analysis and design of turns in alpha-helical hairpins
      Engel, D.E.,Lahr, S.J.,Stayrook, S.E.,Geremia, S.,DeGrado, W.F.
      () TO BE PUBLISHED --: --
    • Proton and metal ion-dependent assembly of a model diiron protein
      Pasternak, A.,Kaplan, J.,Lear, J.D.,Degrado, W.F.
      (2001) Protein Sci. 10: 958
    • Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins
      Lombardi, A.,Summa, C.M.,Geremia, S.,Randaccio, L.,Pavone, V.,DeGrado, W.F.
      (2000) Proc.Natl.Acad.Sci.USA 97: 6298


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Four-helix bundle model
A, B
49N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy 
  • Olderado: 1U7J Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance