4OH2

Crystal Structure of Cu/Zn Superoxide Dismutase I149T

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.384 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Copper-Based Pulsed Dipolar ESR Spectroscopy as a Probe of Protein Conformation Linked to Disease States.

Merz, G.E., Borbat, P.P., Pratt, A.J., Getzoff, E.D., Freed, J.H., Crane, B.R.

(2014) Biophys.J. 107: 1669-1674

  • DOI: 10.1016/j.bpj.2014.07.068

  • PubMed Abstract: 

    • We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. A ...

    We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. Although the extent and the anisotropy of the Cu ESR spectrum provides challenges for PDS, Ku-band (17.3 GHz) double electron-electron resonance and double-quantum coherence variants of PDS coupled with distance reconstruction methods recover Cu-Cu distances in good agreement with crystal structures. Moreover, Cu-PDS measurements expose distinct differences between the conformational properties of wild-type SOD1 and a single-residue variant (I149T) that leads to the disease amyotrophic lateral sclerosis (ALS). The I149T protein displays a broader Cu-Cu distance distribution within the SOD1 dimer compared to wild-type. In a nitroxide (NO)-labeled sample, distance distributions obtained from Cu-Cu, Cu-NO, and NO-NO separations reveal increased structural heterogeneity within the protein and a tendency for mutant dimers to associate. In contrast, perturbations caused by the ALS mutation are completely masked in the crystal structure of I149T. Thus, PDS readily detects alterations in metalloenzyme solution properties not easily deciphered by other methods and in doing so supports the notion that increased range of motion and associations of SOD1 ALS variants contribute to disease progression.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Cu-Zn]
A, B, C, D, E, F, G, H, I, J
153Homo sapiensMutation(s): 3 
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
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.384 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 165.099α = 90.00
b = 203.811β = 90.00
c = 144.407γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Advisory, Refinement description