1HL5

The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Structure of Holo and Metal-Deficient Wild-Type Human Cu, Zn Superoxide Dismutase and its Relevance to Familial Amyotrophic Lateral Sclerosis

Strange, R.W.Antonyuk, S.Hough, M.A.Doucette, P.Rodriguez, J.Hart, P.J.Hayward, L.J.Valentine, J.S.Hasnain, S.S.

(2003) J Mol Biol 328: 877

  • DOI: 10.1016/s0022-2836(03)00355-3
  • Primary Citation of Related Structures:  
    1HL4, 1HL5

  • PubMed Abstract: 
  • Cu, Zn superoxide dismutase (SOD1) forms a crucial component of the cellular defence against oxidative stress. Zn-deficient wild-type and mutant human SOD1 have been implicated in the disease familial amyotrophic lateral sclerosis (FALS). We present here the crystal structures of holo and metal-deficient (apo) wild-type protein at 1 ...

    Cu, Zn superoxide dismutase (SOD1) forms a crucial component of the cellular defence against oxidative stress. Zn-deficient wild-type and mutant human SOD1 have been implicated in the disease familial amyotrophic lateral sclerosis (FALS). We present here the crystal structures of holo and metal-deficient (apo) wild-type protein at 1.8A resolution. The P21 wild-type holo enzyme structure has nine independently refined dimers and these combine to form a "trimer of dimers" packing motif in each asymmetric unit. There is no significant asymmetry between the monomers in these dimers, in contrast to the subunit structures of the FALS G37R mutant of human SOD1 and in bovine Cu,Zn SOD. Metal-deficient apo SOD1 crystallizes with two dimers in the asymmetric unit and shows changes in the metal-binding sites and disorder in the Zn binding and electrostatic loops of one dimer, which is devoid of metals. The second dimer lacks Cu but has approximately 20% occupancy of the Zn site and remains structurally similar to wild-type SOD1. The apo protein forms a continuous, extended arrangement of beta-barrels stacked up along the short crystallographic b-axis, while perpendicular to this axis, the constituent beta-strands form a zig-zag array of filaments, the overall arrangement of which has a similarity to the common structure associated with amyloid-like fibrils.


    Organizational Affiliation

    Molecular Biophysics Group, Department of Synchrotron Radiation, CCLRC Daresbury Laboratory, Warrington, Cheshire, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R [auth S]
153Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D] , AB [auth P] , CB [auth Q] , DA [auth E] , EB [auth S] , FA [auth F] , HA [auth G] , JA [auth H] , 
AA [auth D],  AB [auth P],  CB [auth Q],  DA [auth E],  EB [auth S],  FA [auth F],  HA [auth G],  JA [auth H],  LA [auth I],  NA [auth J],  PA [auth K],  RA [auth L],  T [auth A],  TA [auth M],  V [auth B],  VA [auth N],  X [auth C],  XA [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
BB [auth Q] , CA [auth E] , DB [auth S] , EA [auth F] , GA [auth G] , IA [auth H] , KA [auth I] , MA [auth J] , 
BB [auth Q],  CA [auth E],  DB [auth S],  EA [auth F],  GA [auth G],  IA [auth H],  KA [auth I],  MA [auth J],  OA [auth K],  QA [auth L],  S [auth A],  SA [auth M],  U [auth B],  UA [auth N],  W [auth C],  WA [auth O],  Z [auth D],  ZA [auth P]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth D], Y [auth C], YA [auth O]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.871α = 90
b = 172.38β = 93.45
c = 112.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance