PDBsum entry 3ecv

Go to PDB code: 
protein Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
153 a.a. *
126 a.a. *
Waters ×249
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the als-related pathological mutant i113t of human apo cu,zn superoxide dismutase (sod1)
Structure: Superoxide dismutase [cu-zn]. Chain: a, b, c, d. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.242     R-free:   0.277
Authors: V.Calderone
Key ref:
L.Banci et al. (2009). Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants. Proc Natl Acad Sci U S A, 106, 6980-6985. PubMed id: 19369197 DOI: 10.1073/pnas.0809845106
02-Sep-08     Release date:   19-May-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 a.a.*
Protein chains
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
154 a.a.
126 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   20 terms 
  Biological process     cellular response to potassium ion   66 terms 
  Biochemical function     antioxidant activity     13 terms  


DOI no: 10.1073/pnas.0809845106 Proc Natl Acad Sci U S A 106:6980-6985 (2009)
PubMed id: 19369197  
Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants.
L.Banci, I.Bertini, M.Boca, V.Calderone, F.Cantini, S.Girotto, M.Vieru.
The structural and dynamical properties of the metal-free form of WT human superoxide dismutase 1 (SOD1) and its familial amyotrophic lateral sclerosis (fALS)-related mutants, T54R and I113T, were characterized both in solution, through NMR, and in the crystal, through X-ray diffraction. We found that all 3 X-ray structures show significant structural disorder in 2 loop regions that are, at variance, well defined in the fully-metalated structures. Interestingly, the apo state crystallizes only at low temperatures, whereas all 3 proteins in the metalated form crystallize at any temperature, suggesting that crystallization selects one of the most stable conformations among the manifold adopted by the apo form in solution. Indeed, NMR experiments show that the protein in solution is highly disordered, sampling a large range of conformations. The large conformational variability of the apo state allows the free reduced cysteine Cys-6 to become highly solvent accessible in solution, whereas it is essentially buried in the metalated state and the crystal structures. Such solvent accessibility, together with that of Cys-111, accounts for the tendency to oligomerization of the metal-free state. The present results suggest that the investigation of the solution state coupled with that of the crystal state can provide major insights into SOD1 pathway toward oligomerization in relation to fALS.
  Selected figure(s)  
Figure 1.
Packing of molecules in apo WT SOD1. (A) The apo protein has an extended sheet of β-barrels arranged in the ac plane. Monomer A is shown in blue, monomer B is in yellow, monomer C is in light green, and monomer D is in violet. (B) Contacts between neighboring dimers: H bonds involving OD1 and ND1 of Asn-26 and the O atom of Pro-66 are symmetrically present between monomers A and D. ND1 atom of Asn-26 of monomers C forms an H bond with the O atoms of Val-103, Ile-104, and Ser-102 of monomer B. H bond is shown between OE2 atom of Glu-24 and OD2 atom of Asp-109. H-bonding network is present between molecules in adjacent asymmetric units: the O atom of Lys-128 in monomer A forms H bonds with the N and O atoms of Asn-86 of monomer D1. The O atom of Gly-129 has H bonds to the O atom of Asn-86 and to the OG1 atoms of Thr-88. The N and O atoms of Gly-130 participate in 3 H bonds: to Asn-86 O and to Ser-98 N and O atoms, respectively. Finally, the N atom of Asn-131 forms a weak H-bond to the O atom of Ser-98. (C) The view obtained after rotating A twice by 90° showing the zigzag arrangement of the constituent β-strands aligned along the long ac diagonal of the unit cell.
Figure 2.
Secondary structural elements (red) based on the chemical shift index analysis for the apo WT SOD1 protein. Backbone long range NOEs (blue sticks) determined from 15N-edited NOESY spectra. The locations of the free cysteines Cys-6 and Cys-111 are represented by green and yellow spheres, respectively. The oxidation state of SOD1 cysteine residues was also investigated through ^13C 1D NMR spectra (Fig. S2).
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21120240 I.Choi, Y.S.Huh, and D.Erickson (2011).
Size-selective concentration and label-free characterization of protein aggregates using a Raman active nanofluidic device.
  Lab Chip, 11, 632-638.  
20808835 J.Yin, S.Hu, W.Jiang, L.Liu, S.Lan, X.Song, and C.Liu (2010).
DNA-triggered aggregation of copper, zinc superoxide dismutase in the presence of ascorbate.
  PLoS One, 5, e12328.  
20333435 L.Banci, I.Bertini, F.Cantini, and S.Ciofi-Baffoni (2010).
Cellular copper distribution: a mechanistic systems biology approach.
  Cell Mol Life Sci, 67, 2563-2589.  
19707851 K.A.Jellinger (2009).
Recent advances in our understanding of neurodegeneration.
  J Neural Transm, 116, 1111-1162.  
19828437 K.Teilum, M.H.Smith, E.Schulz, L.C.Christensen, G.Solomentsev, M.Oliveberg, and M.Akke (2009).
Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization.
  Proc Natl Acad Sci U S A, 106, 18273-18278.  
19619132 V.Tõugu, A.Karafin, K.Zovo, R.S.Chung, C.Howells, A.K.West, and P.Palumaa (2009).
Zn(II)- and Cu(II)-induced non-fibrillar aggregates of amyloid-beta (1-42) peptide are transformed to amyloid fibrils, both spontaneously and under the influence of metal chelators.
  J Neurochem, 110, 1784-1795.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.