6SPA | pdb_00006spa

A4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 IN C2 SPACE GROUP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.196 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6SPA

This is version 1.2 of the entry. See complete history

Literature

Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy.

Chantadul, V.Wright, G.S.A.Amporndanai, K.Shahid, M.Antonyuk, S.V.Washbourn, G.Rogers, M.Roberts, N.Pye, M.O'Neill, P.M.Hasnain, S.S.

(2020) Commun Biol 3: 97-97

  • DOI: https://doi.org/10.1038/s42003-020-0826-3
  • Primary Citation Related Structures: 
    6SPA, 6SPH, 6SPI, 6SPJ, 6SPK

  • PubMed Abstract: 

    Mutations to the gene encoding superoxide dismutase-1 (SOD1) were the first genetic elements discovered that cause motor neuron disease (MND). These mutations result in compromised SOD1 dimer stability, with one of the severest and most common mutations Ala4Val (A4V) displaying a propensity to monomerise and aggregate leading to neuronal death. We show that the clinically used ebselen and related analogues promote thermal stability of A4V SOD1 when binding to Cys111 only. We have developed a A4V SOD1 differential scanning fluorescence-based assay on a C6S mutation background that is effective in assessing suitability of compounds. Crystallographic data show that the selenium atom of these compounds binds covalently to A4V SOD1 at Cys111 at the dimer interface, resulting in stabilisation. This together with chemical amenability for hit expansion of ebselen and its on-target SOD1 pharmacological chaperone activity holds remarkable promise for structure-based therapeutics for MND using ebselen as a template.


  • Organizational Affiliation
    • Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.

Macromolecule Content 

  • Total Structure Weight: 96.96 kDa 
  • Atom Count: 8,368 
  • Modeled Residue Count: 918 
  • Deposited Residue Count: 918 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]153Homo sapiensMutation(s): 1 
Gene Names: SOD1
EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
W [auth G]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth L]
H [auth A]
I [auth A]
L [auth C]
M [auth C]
BA [auth L],
H [auth A],
I [auth A],
L [auth C],
M [auth C],
P [auth E],
Q [auth E],
R [auth E],
T [auth G],
U [auth G],
V [auth G],
Y [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
AA [auth L],
J [auth A],
N [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A]
K [auth C]
O [auth E]
S [auth G]
X [auth J]
G [auth A],
K [auth C],
O [auth E],
S [auth G],
X [auth J],
Z [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.196 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.6α = 90
b = 195.96β = 97.1
c = 75.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary