1IJ1

GCN4-pVLT Coiled-coil Trimer with Threonine at the d(12) Position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Buried polar residues in coiled-coil interfaces.

Akey, D.L.Malashkevich, V.N.Kim, P.S.

(2001) Biochemistry 40: 6352-6360

  • DOI: 10.1021/bi002829w
  • Primary Citation of Related Structures:  
    1IJ1, 1IJ0, 1IJ3, 1IJ2

  • PubMed Abstract: 
  • Coiled coils, estimated to constitute 3-5% of the encoded residues in most genomes, are characterized by a heptad repeat, (abcdefg)(n), where the buried a and d positions form the interface between multiple alpha-helices. Although generally hydrophobic, a substantial fraction ( approximately 20%) of these a- and d-position residues are polar or charged ...

    Coiled coils, estimated to constitute 3-5% of the encoded residues in most genomes, are characterized by a heptad repeat, (abcdefg)(n), where the buried a and d positions form the interface between multiple alpha-helices. Although generally hydrophobic, a substantial fraction ( approximately 20%) of these a- and d-position residues are polar or charged. We constructed variants of the well-characterized coiled coil GCN4-p1 with a single polar residue (Asn, Gln, Ser, or Thr) at either an a or a d position. The stability and oligomeric specificity of each variant were measured, and crystal structures of coiled-coil trimers with threonine or serine at either an a or a d position were determined. The structures show how single polar residues in the interface affect not only local packing, but also overall coiled-coil geometry as seen by changes in the Crick supercoil parameters and core cavity volumes.


    Related Citations: 
    • X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
      O'Shea, E.K., Klemm, J.D., Kim, P.S., Alber, T.
      (1991) Science 254: 539
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
      Harbury, P.B., Zhang, T., Kim, P.S., Alber, T.
      (1993) Science 262: 1401
    • Buried polar residues and structural specificity in the GCN4 leucine zipper
      Gonzalez Jr., L., Woolfson, D.N., Alber, T.
      (1996) Nat Struct Biol 3: 1011

    Organizational Affiliation

    Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GENERAL CONTROL PROTEIN GCN4A, B, C34N/AMutation(s): 2 
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.683α = 90
b = 42.192β = 98.87
c = 42.682γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description