Structure and chemical shifts of Cu(I),Zn(II) superoxide dismutase by solid-state NMR

Experimental Data Snapshot

  • Conformers Calculated: 80 
  • Conformers Submitted: 19 
  • Selection Criteria: target function 

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Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

Knight, M.J.Pell, A.J.Bertini, I.Felli, I.C.Gonnelli, L.Pierattelli, R.Herrmann, T.Emsley, L.Pintacuda, G.

(2012) Proc Natl Acad Sci U S A 109: 11095-11100

  • DOI: https://doi.org/10.1073/pnas.1204515109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

  • Organizational Affiliation

    Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Unité Mixte de Recherche 5280 Centre National de la Recherche Scientifique/Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]153Homo sapiensMutation(s): 2 
Gene Names: SOD1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CU

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Conformers Calculated: 80 
  • Conformers Submitted: 19 
  • Selection Criteria: target function 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other