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: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly.

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

(2000) Proc Natl Acad Sci U S A 97: 9907-9912

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

  • 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 problem by stepwise engineering a beta-AP homology into a soluble scaffold, the monomeric protein S6 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6A101Thermus thermophilusMutation(s): 4 
Gene Names: rpsF, rps6
UniProt
Find proteins for P23370 (Thermus thermophilus)
Explore P23370 
Go to UniProtKB:  P23370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23370
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.701α = 90
b = 49.701β = 90
c = 73.255γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2018-12-12
    Changes: Data collection, Database references, Source and taxonomy, Structure summary