1U7M

Solution structure of a diiron protein model: Due Ferri(II) turn mutant


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:  
    1MFT, 1U7J, 1U7M, 1Y47

  • 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 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 ...

    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: 
    • Solution characterization of diiron proteins containing two distinct types of inter-helical loops
      Maglio, O., Nastri, F., Calhoun, J.R., Lahr, S., Pavone, V., DeGrado, W.F., Lombardi, A.
      () 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 U S A 97: 6298
    • 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 U S A 100: 3772

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Four-helix bundle modelA, B53Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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: 1U7M Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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