4NJ0 | pdb_00004nj0

GCN4-p1 single Val9 to Ile mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.283 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4NJ0

This is version 1.2 of the entry. See complete history

Literature

Tuning assembly size in Peptide-based supramolecular polymers by modulation of subunit association affinity.

Oshaben, K.M.Horne, W.S.

(2014) Biomacromolecules 15: 1436-1442

  • DOI: https://doi.org/10.1021/bm5000423
  • Primary Citation Related Structures: 
    4NIZ, 4NJ0, 4NJ1, 4NJ2

  • PubMed Abstract: 

    Nature uses proteins and nucleic acids to form a wide array of functional architectures, and scientists have found inspiration from these structures in the rational design of synthetic biomaterials. We have recently shown that a modular subunit consisting of two α-helical coiled coil peptides attached at their midpoints by an organic linking group can spontaneously self-assemble in aqueous solution to form a soluble supramolecular polymer. Here we explore the use of coiled-coil association affinity, readily tuned by amino acid sequence, as a means to predictably alter properties of these supramolecular assemblies. A series of dimeric coiled-coil peptide sequences with identical quaternary folded structures but systematically altered folded stability were designed and biophysically characterized. The sequences were cross-linked to generate a series of branched, self-assembling biomacromolecular subunits. A clear relationship is observed between coiled-coil association affinity and apparent hydrodynamic diameter of the supramolecular polymers formed by these subunits. Our results provide a family of soluble supramolecular polymers of tunable size and well-characterized coiled-coil sequences that add to the library of building blocks available for use in the rational design of protein-based supramolecular biomaterials.


  • Organizational Affiliation
    • Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.

Macromolecule Content 

  • Total Structure Weight: 8.09 kDa 
  • Atom Count: 557 
  • Modeled Residue Count: 66 
  • Deposited Residue Count: 70 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
General control protein GCN4
A, B
35Saccharomyces cerevisiae S288CMutation(s): 3 
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: 1.90 Å
  • R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.199α = 90
b = 30.41β = 102.01
c = 27.788γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary