1SWI

GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A COMPLEXED WITH BENZENE

• PDB DOI: https://doi.org/10.2210/pdb1SWI/pdb

• Classification: LEUCINE ZIPPER
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 1996-05-09 Released: 1996-11-08 
• Deposition Author(s): Gonzalez, L., Plecs, J., Alber, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

An engineered allosteric switch in leucine-zipper oligomerization.

Gonzalez Jr., L., Plecs, J.J., Alber, T.

(1996) Nat Struct Biol 3: 510-515

• PubMed: 8646536 
• DOI: https://doi.org/10.1038/nsb0696-510
• Primary Citation of Related Structures:  
  1SWI


• PubMed Abstract: 
  

  Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide-benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.

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Organizational Affiliation: 

Department of Molecular and cell Biology, University of California, Berkeley,94720-3206, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.97 kDa 
• Atom Count: 789 
• Modelled Residue Count: 91 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4P1	A, B, C	33	Saccharomyces cerevisiae	Mutation(s): 1
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNZ	D [auth B]	BENZENE C6 H6 UHOVQNZJYSORNB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BNZ	PDBBind:  1SWI	Kd: 8.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.21	α = 90
b = 46.41	β = 90
c = 52.05	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
TNT	refinement
X-PLOR	model building
R-AXIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Gonzalez, L., Plecs, J., Alber, T.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection
• Version 1.5: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.6: 2024-02-14
  Changes: Data collection