6FLH

Monomeric Human Cu,Zn Superoxide dismutase, SOD1 7+7, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Cost of Long Catalytic Loops in Folding and Stability of the ALS-Associated Protein SOD1.

Yang, F.Wang, H.Logan, D.T.Mu, X.Danielsson, J.Oliveberg, M.

(2018) J.Am.Chem.Soc. 140: 16570-16579

  • DOI: 10.1021/jacs.8b08141

  • PubMed Abstract: 
  • A conspicuous feature of the ALS-associated protein SOD1 is that its maturation into a functional enzyme relies on local folding of two disordered loops into a catalytic subdomain. To drive the disorder-to-order transition, the protein employs a sing ...

    A conspicuous feature of the ALS-associated protein SOD1 is that its maturation into a functional enzyme relies on local folding of two disordered loops into a catalytic subdomain. To drive the disorder-to-order transition, the protein employs a single Zn2+ ion. The question is then if the entropic penalty of maintaining such disordered loops in the immatureapoSOD1 monomer is large enough to explain its unusually low stability, slow folding and pathological aggregation in ALS. To find out, we determined the effects of systematically altering the SOD1-loop lengths by protein re-design. The results show that the loops destabilise the apoSOD1 monomer by ≈ 3 kcal/mol, rendering the protein marginally stable and accounting for its aggregation behaviour. Yet the effect on the global folding kinetics remains much smaller with a transition-state destabilisation of < 1 kcal/mol. Notably, this 1/3 transition-state to folded-state stability ratio provides a clear-cut example of the enigmatic disagreement between the Leffler α value from loop-length alterations (typically 1/3) and the 'standard' reaction coordinates based on solvent perturbations (typically > 2/3). Reconciling the issue, we demonstrate that the disagreement disappears when accounting for the progressive loop shortening that occurs along the folding pathway. The approach assumes a consistent Flory loop entropy scaling factor of c = 1.48 for both equilibrium and kinetic data, and has the added benefit of verifying the tertiary interactions of the folding nucleus as determined by phi-value analysis. Thus, SOD1 represents not only a case where evolution of key catalytic function has come with the drawback of a destabilised apo state, but also stands out as a well-suited model system for exploring the physicochemical details of protein self organisation.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Cu-Zn]
A
118Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens)
Go to Gene View: SOD1
Go to UniProtKB:  P00441
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 83.214α = 90.00
b = 83.214β = 90.00
c = 133.478γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Advisory, Data collection, Database references