1BYZ

DESIGNED PEPTIDE ALPHA-1, P1 FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.105 
  • R-Value Observed: 0.085 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle.

Prive, G.G.Anderson, D.H.Wesson, L.Cascio, D.Eisenberg, D.

(1999) Protein Sci 8: 1400-1409

  • DOI: 10.1110/ps.8.7.1400
  • Primary Citation of Related Structures:  
    1BYZ

  • PubMed Abstract: 
  • A 12-residue peptide designed to form an alpha-helix and self-associate into an antiparallel 4-alpha-helical bundle yields a 0.9 A crystal structure revealing unanticipated features. The structure was determined by direct phasing with the "Shake-and-Bake" program, and contains four crystallographically distinct 12-mer peptide molecules plus solvent for a total of 479 atoms ...

    A 12-residue peptide designed to form an alpha-helix and self-associate into an antiparallel 4-alpha-helical bundle yields a 0.9 A crystal structure revealing unanticipated features. The structure was determined by direct phasing with the "Shake-and-Bake" program, and contains four crystallographically distinct 12-mer peptide molecules plus solvent for a total of 479 atoms. The crystal is formed from nearly ideal alpha-helices hydrogen bonded head-to-tail into columns, which in turn pack side-by-side into sheets spanning the width of the crystal. Within each sheet, the alpha-helices run antiparallel and are closely spaced (9-10 A center-to-center). The sheets are more loosely packed against each other (13-14 A between helix centers). Each sheet is amphiphilic: apolar leucine side chains project from one face, charged lysine and glutamate side chains from the other face. The sheets are stacked with two polar faces opposing and two apolar faces opposing. The result is a periodic biomaterial composed of packed protein bilayers, with alternating polar and apolar interfaces. All of the 30 water molecules in the unit cell lie in the polar interface or between the stacked termini of helices. A section through the sheet reveals that the helices packed at the apolar interface resemble the four-alpha-helical bundle of the design, but the helices overhang parts of the adjacent bundles, and the helix crossing angles are less steep than intended (7-11 degrees rather than 18 degrees).


    Related Citations: 
    • Centrosymmetric Bilayers in the 0.75A Resolution Structure of a Designed Alpha- Helical Peptide, D, L-Alpha-1
      Patterson, W.R., Anderson, D.H., Degrado, W.F., Cascio, D., Eisenberg, D.
      (1999) Protein Sci 8: 1410
    • Crystal Structure of Alpha-1: Implications for Protein Design
      Hill, C.P., Anderson, D.H., Wesson, L., Degrado, W.F., Eisenberg, D.
      (1990) Science 249: 543
    • The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide
      Eisenberg, D., Wilcox, W., Eshita, S.M., Pryciak, P.M., Ho, S.P., De Grado, W.F.
      (1986) Proteins 1: 16

    Organizational Affiliation

    Ontario Cancer Institute, University of Toronto, Canada.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1")A, B, C, D13synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
J [auth D](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A], G [auth B], K [auth D](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ETA
Query on ETA

Download Ideal Coordinates CCD File 
E [auth A], I [auth C]ETHANOLAMINE
C2 H7 N O
HZAXFHJVJLSVMW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.105 
  • R-Value Observed: 0.085 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.846α = 102.4
b = 20.909β = 95.33
c = 27.057γ = 119.62
Software Package:
Software NamePurpose
SHAKEmodel building
SnBphasing
SHELXLrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-05-30
    Changes: Data collection, Experimental preparation, Source and taxonomy, Structure summary