1QJH

Protein Aggregation and Alzheimer's Disease: Crystallographic Analysis of the Phenomenon. Engineered version of the ribosomal protein S6 used as a stable scaffold to study oligomerization.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Designed Protein Tetramer Zipped Together with a Hydrophobic Alzheimer Homology: A Structural Clue to Amyloid Assembly

Kristensen, O.Otzen, D.E.Oliveberg, M.

(2000) Proc.Natl.Acad.Sci.USA 97: 9907

  • DOI: 10.1073/pnas.160086297
  • Primary Citation of Related Structures:  1CQM, 1CQN

  • PubMed Abstract: 
  • Limited solubility and precipitation of amyloidogenic sequences such as the Alzheimer peptide (beta-AP) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. Here we have circumvented the solubility proble ...

    Limited solubility and precipitation of amyloidogenic sequences such as the Alzheimer peptide (beta-AP) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. Here we have circumvented the solubility problem by stepwise engineering a beta-AP homology into a soluble scaffold, the monomeric protein S6. The S6 construct with the highest beta-AP homology crystallizes as a tetramer that is linked by the beta-AP residues forming intermolecular antiparallel beta-sheets. This construct also shows increased coil aggregation during refolding, and a 14-mer peptide encompassing the engineered sequence forms fibrils. Mutational analysis shows that intermolecular association is linked to the overall hydrophobicity of the sticky sequence and implies the existence of "structural gatekeepers" in the wild-type protein, that is, charged side chains that prevent aggregation by interrupting contiguous stretches of hydrophobic residues in the primary sequence.


    Related Citations: 
    • Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus
      Lindahl, M.,Svensson, L.A.,Liljas, A.,Sedelnikova, S.E.,Eliseikina, I.A.,Fomenkova, N.P.,Nevskaya, N.,Nikonov, S.V.,Garber, M.B.,Muranova, T.A.,Rykonova, A.I.,Amons, R.
      (1994) Embo J. 13:6: 1249


    Organizational Affiliation

    Department of Biochemistry, Umeâ University, S-901 87 Umeâ, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S6
A
101Thermus thermophilusGene Names: rpsF (rps6)
Find proteins for P23370 (Thermus thermophilus)
Go to UniProtKB:  P23370
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.701α = 90.00
b = 49.701β = 90.00
c = 73.255γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection