4E0Q | pdb_00004e0q

Crystal structure of MPN domain from COP9 signalosome

• PDB DOI: https://doi.org/10.2210/pdb4E0Q/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-05 Released: 2012-03-21 
• Deposition Author(s): Zhang, H., Gao, Z.Q., Dong, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.261 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6

Zhang, H., Gao, Z.Q., Wang, W.J., Liu, G.F., Shtykova, E.V., Xu, J.H., Li, L.F., Su, X.D., Dong, Y.H.

(2012) FEBS Lett 586: 1147-1153

• PubMed: 22575649 
• DOI: https://doi.org/10.1016/j.febslet.2012.03.029
• Primary Citation Related Structures: 
  4E0Q


• PubMed Abstract: 
  

  The COP9 signalosome (CSN) is a multiprotein complex containing eight subunits and is highly conserved from fungi to human. CSN is proposed to widely participate in many physiological processes, including protein degradation, DNA damage response and signal transduction. Among those subunits, only CSN5 and CSN6 belong to JAMM family. CSN5 possesses isopeptidase activity, but CSN6 lacks this ability. Here we report the 2.5Å crystal structure of MPN domain from Drosophila melanogaster CSN6. Structural comparison with other MPN domains, along with bioinformation analysis, suggests that MPN domain from CSN6 may serve as a scaffold instead of a metalloprotease.

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Organizational Affiliation: 
• State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.88 kDa 
• Atom Count: 1,915 
• Modeled Residue Count: 231 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 6	A, B	141	Drosophila melanogaster	Mutation(s): 0  Gene Names: CSN6, CG6932
UniProt
Find proteins for Q9VCY3 (Drosophila melanogaster) Explore Q9VCY3  Go to UniProtKB:  Q9VCY3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.261 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.062	α = 90
b = 109.062	β = 90
c = 46.437	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Zhang, H., Gao, Z.Q., Dong, Y.H.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2012-11-21
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary