2IPZ

A Parallel Coiled-Coil Tetramer with Offset Helices


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

A Parallel Coiled-Coil Tetramer with Offset Helices.

Liu, J.Deng, Y.Zheng, Q.Cheng, C.S.Kallenbach, N.R.Lu, M.

(2006) Biochemistry 45: 15224-15231

  • DOI: https://doi.org/10.1021/bi061914m
  • Primary Citation of Related Structures:  
    2IPZ

  • PubMed Abstract: 

    Specific helix-helix interactions are fundamental in assembling the native state of proteins and in protein-protein interfaces. Coiled coils afford a unique model system for elucidating principles of molecular recognition between alpha helices. The coiled-coil fold is specified by a characteristic seven amino acid repeat containing hydrophobic residues at the first (a) and fourth (d) positions. Nonpolar side chains spaced three and four residues apart are referred to as the 3-4 hydrophobic repeat. The presence of apolar amino acids at the e or g positions (corresponding to a 3-3-1 hydrophobic repeat) can provide new possibilities for close-packing of alpha-helices that includes examples such as the lac repressor tetramerization domain. Here we demonstrate that an unprecedented coiled-coil interface results from replacement of three charged residues at the e positions in the dimeric GCN4 leucine zipper by nonpolar valine side chains. Equilibrium circular dichroism and analytical ultracentrifugation studies indicate that the valine-containing mutant forms a discrete alpha-helical tetramer with a significantly higher stability than the parent leucine-zipper molecule. The 1.35 A resolution crystal structure of the tetramer reveals a parallel four-stranded coiled coil with a three-residue interhelical offset. The local packing geometry of the three hydrophobic positions in the tetramer conformation is completely different from that seen in classical tetrameric structures yet bears resemblance to that in three-stranded coiled coils. These studies demonstrate that distinct van der Waals interactions beyond the a and d side chains can generate a diverse set of helix-helix interfaces and three-dimensional supercoil structures.


  • Organizational Affiliation

    Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
General control protein GCN4
A, B, C, D
34Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCN4
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03069
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.783α = 90
b = 53.878β = 95.77
c = 52.016γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-01-16 
  • Deposition Author(s): Liu, J., Lu, M.

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description