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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.03.029
Primary Citation of 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.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VCY3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Zhang, H.

Gao, Z.Q.

Dong, Y.H.

Revision History (Full details and data files)

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