3TXM

Crystal structure of Rpn6 from Drosophila melanogaster, Gd(3+) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together.

Pathare, G.R.Nagy, I.Bohn, S.Unverdorben, P.Hubert, A.Korner, R.Nickell, S.Lasker, K.Sali, A.Tamura, T.Nishioka, T.Forster, F.Baumeister, W.Bracher, A.

(2012) Proc.Natl.Acad.Sci.USA 109: 149-154

  • DOI: 10.1073/pnas.1117648108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteasomes execute the degradation of most cellular proteins. Although the 20S core particle (CP) has been studied in great detail, the structure of the 19S regulatory particle (RP), which prepares ubiquitylated substrates for degradation, has remai ...

    Proteasomes execute the degradation of most cellular proteins. Although the 20S core particle (CP) has been studied in great detail, the structure of the 19S regulatory particle (RP), which prepares ubiquitylated substrates for degradation, has remained elusive. Here, we report the crystal structure of one of the RP subunits, Rpn6, and we describe its integration into the cryo-EM density map of the 26S holocomplex at 9.1 Å resolution. Rpn6 consists of an α-solenoid-like fold and a proteasome COP9/signalosome eIF3 (PCI) module in a right-handed suprahelical configuration. Highly conserved surface areas of Rpn6 interact with the conserved surfaces of the Pre8 (alpha2) and Rpt6 subunits from the alpha and ATPase rings, respectively. The structure suggests that Rpn6 has a pivotal role in stabilizing the otherwise weak interaction between the CP and the RP.


    Organizational Affiliation

    Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory complex subunit p42B
A
394Drosophila melanogasterMutation(s): 0 
Gene Names: Rpn6
Find proteins for Q7KLV9 (Drosophila melanogaster)
Go to UniProtKB:  Q7KLV9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GD3
Query on GD3

Download SDF File 
Download CCD File 
A
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 161.251α = 90.00
b = 161.251β = 90.00
c = 42.080γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
SHELXphasing
SCALAdata scaling
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXDphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references
  • Version 1.2: 2012-02-01
    Type: Database references