3MND | pdb_00003mnd

Crystallographic analysis of the cystosolic cu/zn Superoxide dismutase from taenia solium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Cu / Zn superoxide dismutase from Taenia solium reveals metal-mediated self-assembly

Hernandez-Santoyo, A.Landa, A.Gonzalez-Mondragon, E.Pedraza-Escalona, M.Parra-Unda, R.Rodriguez-Romero, A.

(2011) FEBS J 278: 3308-3318

  • DOI: https://doi.org/10.1111/j.1742-4658.2011.08247.x
  • Primary Citation Related Structures: 
    3MND

  • PubMed Abstract: 

    Taenia solium is the cestode responsible for porcine and human cysticercosis. The ability of this parasite to establish itself in the host is related to its evasion of the immune response and its antioxidant defence system. The latter includes enzymes such as cytosolic Cu/Zn superoxide dismutase. In this article, we describe the crystal structure of a recombinant T. solium Cu/Zn superoxide dismutase, representing the first structure of a protein from this organism. This enzyme shows a different charge distribution at the entrance of the active channel when compared with human Cu/Zn superoxide dismutase, giving it interesting properties that may allow the design of specific inhibitors against this cestode. The overall topology is similar to other superoxide dismutase structures; however, there are several His and Glu residues on the surface of the protein that coordinate metal ions both intra- and intermolecularly. Interestingly, one of these ions, located on the β2 strand, establishes a metal-mediated intermolecular β-β interaction, including a symmetry-related molecule. The factors responsible for the abnormal protein-protein interactions that lead to oligomerization are still unknown; however, high metal levels have been implicated in these phenomena, but exactly how they are involved remains unclear. The present results suggest that this structure could be useful as a model to explain an alternative mechanism of protein aggregation commonly observed in insoluble fibrillar deposits.


  • Organizational Affiliation
    • Instituto de Química, Universidad Nacional Autónoma de México, México, DF, México. hersan@servidor.unam.mx

Macromolecule Content 

  • Total Structure Weight: 31.87 kDa 
  • Atom Count: 2,329 
  • Modeled Residue Count: 304 
  • Deposited Residue Count: 304 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B
152Taenia soliumMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for Q8WRF5 (Taenia solium)
Explore Q8WRF5 
Go to UniProtKB:  Q8WRF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WRF5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.171α = 90
b = 53.798β = 90
c = 117.264γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary