Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.03 kDa 
• Atom Count: 2221 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

4FF9

Crystal Structure of cysteinylated WT SOD1.

• PDB DOI: 10.2210/pdb4FF9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2012-05-31 Released: 2013-09-04 
• Deposition Author(s): Auclair, J.R., Brodkin, H.R., D'Aquino, J.A., Ringe, D., Petsko, G.A., Agar, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.335 
• R-Value Work: 0.276 
• R-Value Observed: 0.282 

Literature

Structural consequences of cysteinylation of cu/zn-superoxide dismutase.

Auclair, J.R., Brodkin, H.R., D'Aquino, J.A., Petsko, G.A., Ringe, D., Agar, J.N.

(2013) Biochemistry 52: 6145-6150

• PubMed: 23919400 
• DOI: 10.1021/bi400613h
• Primary Citation of Related Structures:  
  4FF9


• PubMed Abstract: 
  

The metalloenzyme Cu/Zn-superoxide dismutase (SOD1) catalyzes the reduction of superoxide anions into molecular oxygen and hydrogen peroxide. Hydrogen peroxide can oxidize SOD1, resulting in aberrant protein conformational changes, disruption of SOD1 function, and DNA damage. Cells may have evolved mechanisms of regulation that prevent such oxidation. We observed that cysteinylation of cysteine 111 (Cys111) of SOD1 prevents oxidation by peroxide (DOI 10.1021/bi4006122 ). In this article, we characterize cysteinylated SOD1 using differential scanning fluorometry and X-ray crystallography. The stoichiometry of binding was one cysteine per SOD1 dimer, and there does not appear to be free volume for a second cysteine without disrupting the dimer interface. Much of the three-dimensional structure of SOD1 is unaffected by cysteinylation. However, local conformational changes are observed in the cysteinylated monomer that include changes in conformation of the electrostatic loop (loop VII; residues 133-144) and the dimer interface (loop VI; residues 102-115). In addition, our data shows how cysteinylation precludes oxidation of cysteine 111 and suggests possible cross-talk between the dimer interface and the electrostatic loop.

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Organizational Affiliation: 

Departments of Biochemistry and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	153	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	C [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	E [auth A], G [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.335 
• R-Value Work: 0.276 
• R-Value Observed: 0.282 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.05	α = 90
b = 113.05	β = 90
c = 70.59	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-31 
• Released Date: 2013-09-04 
Deposition Author(s): Auclair, J.R., Brodkin, H.R., D'Aquino, J.A., Ringe, D., Petsko, G.A., Agar, J.N.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references