3IPM

Crystal Structure of Archaeal 20S Proteasome in Complex with the C-terminus of PAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions.

Yu, Y.Smith, D.M.Kim, H.M.Rodriguez, V.Goldberg, A.L.Cheng, Y.

(2010) EMBO J 29: 692-702

  • DOI: 10.1038/emboj.2009.382
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein degradation in the 20S proteasome is regulated in eukaryotes by the 19S ATPase complex and in archaea by the homologous PAN ATPase ring complex. Subunits of these hexameric ATPases contain on their C-termini a conserved hydrophobic-tyrosine-X ...

    Protein degradation in the 20S proteasome is regulated in eukaryotes by the 19S ATPase complex and in archaea by the homologous PAN ATPase ring complex. Subunits of these hexameric ATPases contain on their C-termini a conserved hydrophobic-tyrosine-X (HbYX) motif that docks into pockets in the 20S to stimulate the opening of a gated substrate entry channel. Here, we report the crystal structure of the archaeal 20S proteasome in complex with the C-terminus of the archaeal proteasome regulatory ATPase, PAN. This structure defines the detailed interactions between the critical C-terminal HbYX motif and the 20S alpha-subunits and indicates that the intersubunit pocket in the 20S undergoes an induced-fit conformational change on binding of the HbYX motif. This structure together with related mutagenesis data suggest how in eukaryotes certain proteasomal ATPases bind to specific pockets in an asymmetrical manner to regulate gate opening.


    Organizational Affiliation

    The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94132, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha
A, B, C, D, E, F, G
233Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmATa1288
EC: 3.4.25.1
Find proteins for P25156 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  P25156

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta
H, I, J, K, L, M, N
217Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmBTa0612
EC: 3.4.25.1
Find proteins for P28061 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  P28061

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
O, P, Q, R, S, T, U
239Trypanosoma bruceiMethanocaldococcus jannaschii
This entity is chimeric
Mutation(s): 1 
Gene Names: Tb10.70.3660
Find proteins for Q38BM8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q38BM8
Find proteins for Q58576 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58576
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.89α = 90
b = 166.89β = 90
c = 412.08γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-08-17 
  • Released Date: 2009-12-29 
  • Deposition Author(s): Yu, Y., Cheng, Y.

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Data collection, Refinement description, Source and taxonomy