Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 18-mer - A9B6C2D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 18-mer - A6B1C1D1E1F1G1H1I1J1K1L1M1 

Local Symmetry: Dihedral - D3  (3D View)
Local Stoichiometry: Homo 6-mer - B6 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - C2 

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

Macromolecule Content

• Total Structure Weight: 112.76 kDa 
• Atom Count: 7,566 
• Modelled Residue Count: 1,009 
• Deposited Residue Count: 1,071 
• Unique protein chains: 5

 3QO6

Crystal structure analysis of the plant protease Deg1

• PDB DOI:  https://doi.org/10.2210/pdb3QO6/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Arabidopsis thaliana, unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-09 Released: 2011-05-04 
• Deposition Author(s): Clausen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.228 

Literature

Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure.

Kley, J., Schmidt, B., Boyanov, B., Stolt-Bergner, P.C., Kirk, R., Ehrmann, M., Knopf, R.R., Naveh, L., Adam, Z., Clausen, T.

(2011) Nat Struct Mol Biol 18: 728-731

• PubMed: 21532594 
• DOI: https://doi.org/10.1038/nsmb.2055
• Primary Citation of Related Structures:  
  3QO6


• PubMed Abstract: 
  

Deg1 is a chloroplastic protease involved in maintaining the photosynthetic machinery. Structural and biochemical analyses reveal that the inactive Deg1 monomer is transformed into the proteolytically active hexamer at acidic pH. The change in pH is sensed by His244, which upon protonation, repositions a specific helix to trigger oligomerization. This system ensures selective activation of Deg1 during daylight, when acidification of the thylakoid lumen occurs and photosynthetic proteins are damaged.

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Organizational Affiliation: 

Research Institute of Molecular Pathology (IMP), Vienna, Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease Do-like 1, chloroplastic	A, B, C	348	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g27925, DEG1, DEGP, DEGP1, K16N12.18 EC: 3.4.21
UniProt
Find proteins for O22609 (Arabidopsis thaliana) Explore O22609  Go to UniProtKB:  O22609

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	D	7	unidentified	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	E, H, I	4	unidentified	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	F	5	unidentified	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	G	3	unidentified	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.228 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.135	α = 90
b = 126.135	β = 90
c = 328.303	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Clausen, T.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-09-05
  Changes: Derived calculations