Sequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

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Conformational specificity of the lac repressor coiled-coil tetramerization domain.

Liu, J.Zheng, Q.Deng, Y.Li, Q.Kallenbach, N.R.Lu, M.

(2007) Biochemistry 46: 14951-14959

  • DOI: https://doi.org/10.1021/bi701930d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Predictive understanding of how the folded, functional shape of a native protein is encoded in the linear sequence of its amino acid residues remains an unsolved challenge in modern structural biology. Antiparallel four-stranded coiled coils are relatively simple protein structures that embody a heptad sequence repeat and rich diversity for tertiary packing of alpha-helices. To explore specific sequence determinants of the lac repressor coiled-coil tetramerization domain, we have engineered a set of buried nonpolar side chains at the a-, d-, and e-positions into the hydrophobic interior of the dimeric GCN4 leucine zipper. Circular dichroism and equilibrium ultracentrifugation studies show that this core variant (GCN4-pAeLV) forms a stable tetrameric structure with a reversible and highly cooperative thermal unfolding transition. The X-ray crystal structure at 1.9 A reveals that GCN4-pAeLV is an antiparallel four-stranded coiled coil of the lac repressor type in which the a, d, and e side chains associate by means of combined knobs-against-knobs and knobs-into-holes packing with a characteristic interhelical offset of 0.25 heptad. Comparison of the side chain shape and packing in the antiparallel tetramers shows that the burial of alanine residues at the e positions between the neighboring helices of GCN4-pAeLV dictates both the antiparallel orientation and helix offset. This study fills in a gap in our knowledge of the determinants of structural specificity in antiparallel coiled coils and improves our understanding of how specific side chain packing forms the teritiary structure of a functional protein.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GCN4 leucine zipper
A, B, C, D, E
A, B, C, D, E, F, G, H
34Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCN4AAS3ARG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CIT

Download Ideal Coordinates CCD File 
K [auth C],
O [auth D],
P [auth G],
Q [auth G]
C6 H8 O7
Query on ZN

Download Ideal Coordinates CCD File 
I [auth C],
L [auth D]
Query on ACT

Download Ideal Coordinates CCD File 
J [auth C],
M [auth D],
N [auth D]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.696α = 90
b = 51.696β = 90
c = 99.793γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-06-17 
  • Deposition Author(s): Liu, J., Lu, M.

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description