Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 0.66 kDa 
• Atom Count: 49 
• Modelled Residue Count: 7 
• Deposited Residue Count: 7 
• Unique protein chains: 1

4NIP

GVIGIAQ segment 147-153 from Human Superoxide Dismutase

• PDB DOI: 10.2210/pdb4NIP/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-11-06 Released: 2013-12-04 
• Deposition Author(s): Sievers, S.A., Sawaya, M.R., Eisenberg, D., Ivanova, M.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS.

Ivanova, M.I., Sievers, S.A., Guenther, E.L., Johnson, L.M., Winkler, D.D., Galaleldeen, A., Sawaya, M.R., Hart, P.J., Eisenberg, D.S.

(2014) Proc Natl Acad Sci U S A 111: 197-201

• PubMed: 24344300 
• DOI: 10.1073/pnas.1320786110
• Primary Citation of Related Structures:  
  4NIN, 4NIO, 4NIP


• PubMed Abstract: 
  

ALS is a terminal disease of motor neurons that is characterized by accumulation of proteinaceous deposits in affected cells. Pathological deposition of mutated Cu/Zn superoxide dismutase (SOD1) accounts for ∼20% of the familial ALS (fALS) cases. However, understanding the molecular link between mutation and disease has been difficult, given that more than 140 different SOD1 mutants have been observed in fALS patients. In addition, the molecular origin of sporadic ALS (sALS) is unclear. By dissecting the amino acid sequence of SOD1, we identified four short segments with a high propensity for amyloid fibril formation. We find that fALS mutations in these segments do not reduce their propensity to form fibrils. The atomic structures of two fibril-forming segments from the C terminus, (101)DSVISLS(107) and (147)GVIGIAQ(153), reveal tightly packed β-sheets with steric zipper interfaces characteristic of the amyloid state. Based on these structures, we conclude that both C-terminal segments are likely to form aggregates if available for interaction. Proline substitutions in (101)DSVISLS(107) and (147)GVIGIAQ(153) impaired nucleation and fibril growth of full-length protein, confirming that these segments participate in aggregate formation. Our hypothesis is that improper protein maturation and incompletely folded states that render these aggregation-prone segments available for interaction offer a common molecular pathway for sALS and fALS.

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Organizational Affiliation: 

Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1570.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GVTGIAQ segment from Superoxide dismutase [Cu-Zn]	A	7	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.128	α = 90
b = 4.843	β = 99.5
c = 18.142	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-06 
• Released Date: 2013-12-04 
Deposition Author(s): Sievers, S.A., Sawaya, M.R., Eisenberg, D., Ivanova, M.I.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description