5J0F | pdb_00005j0f

Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P4/5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.170 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.129 (Depositor) 
  • R-Value Observed: 
    0.131 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5J0F

This is version 1.2 of the entry. See complete history

Literature

Tricking a Protein To Swap Strands.

Wang, H.Lang, L.Logan, D.T.Danielsson, J.Oliveberg, M.

(2016) J Am Chem Soc 138: 15571-15579

  • DOI: https://doi.org/10.1021/jacs.6b05151
  • Primary Citation Related Structures: 
    5J07, 5J0C, 5J0F, 5J0G

  • PubMed Abstract: 

    Despite continuing interest in partly unfolded proteins as precursors for aggregation and adverse gain-of-function in human disease, there is yet little known about the local transitions of native structures that possibly lead to such intermediate states. To target this problem, we present here a protein-design strategy that allows real-time detection of rupture and swapping of complete secondary-structure elements in globular proteins-molecular events that have previously been inaccessible experimental analysis. The approach is applied to the dynamic β-barrel of SOD1, associated with pathologic aggregation in the neurodegenerative disease ALS. Data show that rupture and re-insertion of individual β-strands do not take place locally but require the SOD1 barrel to unfold globally. The finding questions the very existence of partly unfolded intermediates in the SOD1 aggregation process and presents new clues to the mechanism by which hydrogen bonding maintains global structural integrity.


  • Organizational Affiliation
    • Arrhenius Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University , 106 91 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 22.98 kDa 
  • Atom Count: 1,879 
  • Modeled Residue Count: 228 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
A, B
114Homo sapiensMutation(s): 0 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.170 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.129 (Depositor) 
  • R-Value Observed: 0.131 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.72α = 90
b = 71.72β = 90
c = 69.51γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description