Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 11.86 kDa 
• Atom Count: 814 
• Residue Count: 93 
• Unique protein chains: 1

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.

• DOI: 10.2210/pdb1QJH/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-06-24 Released: 2000-06-29 
• Deposition Author(s): Kristensen, O., Otzen, D.E., Oliveberg, M.

---

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 

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

• PubMed: 10944185 
• DOI: 10.1073/pnas.160086297
• Structures With Same Primary Citation


• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	A	101	Thermus thermophilus	Mutation(s): 4  Gene Names: rpsF, rps6
Find proteins for P23370 (Thermus thermophilus) Go to UniProtKB:  P23370

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 49.701	α = 90
b = 49.701	β = 90
c = 73.255	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-06-24 
• Released Date: 2000-06-29 
Deposition Author(s): Kristensen, O., Otzen, D.E., Oliveberg, M.

Revision History 

• 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