5K02

Structure of human SOD1 with T2D mutation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation.

Fay, J.M., Zhu, C., Proctor, E.A., Tao, Y., Cui, W., Ke, H., Dokholyan, N.V.

(2016) Structure 24: 1898-1906

  • DOI: 10.1016/j.str.2016.08.011
  • Primary Citation of Related Structures:  
    5K02

  • PubMed Abstract: 

    • The majority of amyotrophic lateral sclerosis (ALS)-related mutations in the enzyme Cu,Zn superoxide dismutase (SOD1), as well as a post-translational modification, glutathionylation, destabilize the protein and lead to a misfolded oligomer that is toxic to motor neurons ...

    The majority of amyotrophic lateral sclerosis (ALS)-related mutations in the enzyme Cu,Zn superoxide dismutase (SOD1), as well as a post-translational modification, glutathionylation, destabilize the protein and lead to a misfolded oligomer that is toxic to motor neurons. The biophysical role of another physiological SOD1 modification, T2-phosphorylation, has remained a mystery. Here, we find that a phosphomimetic mutation, T2D, thermodynamically stabilizes SOD1 even in the context of a strongly SOD1-destabilizing mutation, A4V, one of the most prevalent and aggressive ALS-associated mutations in North America. This stabilization protects against formation of toxic SOD oligomers and positively impacts motor neuron survival in cellular assays. We solve the crystal structure of T2D-SOD1 and explain its stabilization effect using discrete molecular dynamics (DMD) simulations. These findings imply that T2-phosphorylation may be a plausible innate cellular protection response against SOD1-induced cytotoxicity, and stabilizing the SOD1 native conformation might offer us viable pharmaceutical strategies against currently incurable ALS.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Program in Molecular and Cellular Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: dokh@unc.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
153Homo sapiensMutation(s): 1 
Gene Names: SOD1
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth B],
BB [auth O],
DA [auth C],
DB [auth P],
FA [auth D],
BA [auth B],
BB [auth O],
DA [auth C],
DB [auth P],
FA [auth D],
FB [auth Q],
HA [auth E],
HB [auth R],
JA [auth F],
JB [auth S],
LA [auth G],
LB [auth T],
NA [auth H],
NB [auth U],
PA [auth I],
PB [auth V],
RA [auth J],
RB [auth W],
TA [auth K],
TB [auth X],
VA [auth L],
XA [auth M],
Z [auth A],
ZA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CU
Query on CU
Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth O],
CA [auth C],
CB [auth P],
EA [auth D],
AA [auth B],
AB [auth O],
CA [auth C],
CB [auth P],
EA [auth D],
EB [auth Q],
GA [auth E],
GB [auth R],
IA [auth F],
IB [auth S],
KA [auth G],
KB [auth T],
MA [auth H],
MB [auth U],
OA [auth I],
OB [auth V],
QA [auth J],
QB [auth W],
SA [auth K],
SB [auth X],
UA [auth L],
WA [auth M],
Y [auth A],
YA [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.98α = 89.86
b = 111.961β = 89.85
c = 149.88γ = 60.13
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM080742

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence