5W0J

Antiparallel coiled coil hexamer formed by de novo peptides (ACC-Hex2).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation.

Spencer, R.K.Hochbaum, A.I.

(2017) Biochemistry 56: 5300-5308

  • DOI: 10.1021/acs.biochem.7b00756
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coiled coils are a robust motif for exploring amino acid interactions, generating unique supramolecular structures, and expanding the functional properties of biological materials. A recently discovered antiparallel coiled-coil hexamer (ACC-Hex, pept ...

    Coiled coils are a robust motif for exploring amino acid interactions, generating unique supramolecular structures, and expanding the functional properties of biological materials. A recently discovered antiparallel coiled-coil hexamer (ACC-Hex, peptide 1) exhibits a unique interaction in which Phe and Ile residues from adjacent α-helices interact to form a Phe-Ile zipper within the hydrophobic core. Analysis of the X-ray crystallographic structure of ACC-Hex suggests that the stability of the six-helix bundle relies on specific interactions between the Phe and Ile residues. The Phe-Ile zipper is unprecedented and represents a powerful tool for utilizing the Phe-Ile interactions to direct supramolecular assembly. To further probe and understand the limits of the Phe-Ile zipper, we designed peptide sequences with natural and unnatural amino acids placed at the Phe and Ile residue positions. Using size exclusion chromatography and small-angle X-ray scattering, we found that the proper assembly of ACC-Hex from monomers is sensitive to subtle changes in side chain steric bulk and hydrophobicity introduced by mutations at the Phe and Ile residue positions. Of the sequence variants that formed ACC-Hex, mutations in the hydrophobic core significantly affected the stability of the hexamer, from a ΔGuw of 2-8 kcal mol-1. Additional sequences were designed to further probe and enhance the stability of the ACC-Hex system by maximizing salt bridging between the solvent-exposed residues. Finally, we expanded on the generality of the Phe-Ile zipper, creating a unique sequence that forms an antiparallel hexamer that is topologically similar to ACC-Hex but atomistically unique.


    Organizational Affiliation

    Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine , Irvine, California 92697-2575, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
peptide 1
A, B
29N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYN
Query on LYN

Download SDF File 
Download CCD File 
A, B
2,6-DIAMINO-HEXANOIC ACID AMIDE
C6 H16 N3 O
HKXLAGBDJVHRQG-YFKPBYRVSA-O
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI
A, B
L-PEPTIDE LINKINGC9 H10 I N O2PHE
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 52.560α = 90.00
b = 52.560β = 90.00
c = 93.040γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references
  • Version 1.2: 2017-10-25
    Type: Database references