1L4X

octameric de novo designed peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Removing an interhelical salt bridge abolishes coiled-coil formation in a de novo designed peptide

Meier, M.Lustig, A.Aebi, U.Burkhard, P.

(2002) J.STRUCT.BIOL. 137: 65-72

  • DOI: 10.1006/jsbi.2002.4467

  • PubMed Abstract: 
  • Alpha-helical coiled coils represent a common protein oligomerization motif that are mainly stabilized by hydrophobic interactions occurring along their coiled-coil interface, the so-called hydrophobic seam. We have recently de novo designed and opti ...

    Alpha-helical coiled coils represent a common protein oligomerization motif that are mainly stabilized by hydrophobic interactions occurring along their coiled-coil interface, the so-called hydrophobic seam. We have recently de novo designed and optimized a series of two-heptad repeat long coiled-coil peptides which are further stabilized by a complex network of inter- and intrahelical salt bridges. Here we have extended the de novo design of such two heptad-repeat long peptides by removing the central and most important g-e' Arg to Glu (g-e'RE) ionic interhelical interaction and replacing these residues by alanine residues. The effect of the missing interhelical ionic interaction on coiled-coil formation and stability has been analyzed by CD spectroscopy, analytical ultracentrifugation, and X-ray crystallography. We show that the peptide, while being highly alpha-helical, is no longer able to form a parallel coiled-coil structure but rather assumes an octameric globular helical assembly devoid of any coiled-coil interactions.


    Related Citations: 
    • The Coiled-coil Trigger Site of the Rod Domain of Cortexillin I Unveils a Distinct Network of Interhelical and Intrahelical Salt Bridges
      Burkhard, P.,Kammerer, R.A.,Steinmetz, M.O.,Bourenkov, G.P.,Aebi, U.
      (2000) Structure 8: 223
    • Design of a Minimal Protein Oligomerization Domain by a Structural Approach
      Burkhard, P.,Meier, M.,Lustig, A.
      (2000) Protein Sci. 9: 2294
    • Improving coiled-coil stability by optimizing ionic interactions
      Burkhard, P.,Ivaninskii, S.,Lustig, A.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    M.E. Müller Institute for Structural Biology, University of Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
A, B, C, D, E, F, G, H
16N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C, D, E, F, G, H
NON-POLYMERH2 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.628α = 90.00
b = 56.628β = 90.00
c = 113.869γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation