1N18 | pdb_00001n18

Thermostable mutant of Human Superoxide Dismutase, C6A, C111S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.250 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1N18

This is version 1.4 of the entry. See complete history

Literature

Insights into Lou Gehrig's disease from the structure and instability of the A4V mutant of human Cu,Zn superoxide dismutase.

Cardoso, R.M.F.Thayer, M.M.DiDonato, M.Lo, T.P.Bruns, C.K.Getzoff, E.D.Tainer, J.A.

(2002) J Mol Biology 324: 247-256

  • DOI: https://doi.org/10.1016/s0022-2836(02)01090-2
  • Primary Citation Related Structures: 
    1N18, 1N19

  • PubMed Abstract: 

    Mutations in human superoxide dismutase (HSOD) have been linked to the familial form of amyotrophic lateral sclerosis (FALS). Amyotrophic lateral sclerosis (ALS or Lou Gehrig's disease) is one of the most common neurodegenerative disorders in humans. In ALS patients, selective killing of motor neurons leads to progressive paralysis and death within one to five years of onset. The most frequent FALS mutation in HSOD, Ala4-->Val, is associated with the most rapid disease progression. Here we identify and characterize key differences in the stability between the A4V mutant protein and its thermostable parent (HSOD-AS), in which free cysteine residues were mutated to eliminate interferences from cysteine oxidation. Denaturation studies reveal that A4V unfolds at a guanidine-HCl concentration 1M lower than HSOD-AS, revealing that A4V is significantly less stable than HSOD-AS. Determination and analysis of the crystallographic structures of A4V and HSOD-AS reveal structural features likely responsible for the loss of architectural stability of A4V observed in the denaturation experiments. The combined structural and biophysical results presented here argue that architectural destabilization of the HSOD protein may underlie the toxic function of the many HSOD FALS mutations.


  • Organizational Affiliation
    • Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, Maildrop MB4, 10550 North Torrey Pines Road, La Jolla, CA 92037-1027, USA.

Macromolecule Content 

  • Total Structure Weight: 160.49 kDa 
  • Atom Count: 12,504 
  • Modeled Residue Count: 1,530 
  • Deposited Residue Count: 1,540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
154Homo sapiensMutation(s): 2 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
S [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth H]
CA [auth I]
EA [auth J]
L [auth A]
N [auth B]
AA [auth H],
CA [auth I],
EA [auth J],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
U [auth E],
W [auth F],
Y [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1

Query on CU1



Download:Ideal Coordinates CCD File
BA [auth I]
DA [auth J]
K [auth A]
M [auth B]
O [auth C]
BA [auth I],
DA [auth J],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.250 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.2α = 90
b = 165.2β = 90
c = 144.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary