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 

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This is version 1.4 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: https://doi.org/10.1038/emboj.2009.382
  • Primary Citation of Related Structures:  
    3IPM

  • 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 (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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha
A, B, C, D, E
A, B, C, D, E, F, G
233Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmATa1288
EC: 3.4.25.1
UniProt
Find proteins for P25156 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
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Go to UniProtKB:  P25156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25156
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
H, I, J, K, L
H, I, J, K, L, M, N
217Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmBTa0612
EC: 3.4.25.1
UniProt
Find proteins for P28061 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore P28061 
Go to UniProtKB:  P28061
Entity Groups  
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UniProt GroupP28061
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
O, P, Q, R, S
O, P, Q, R, S, T, U
239Trypanosoma bruceiMethanocaldococcus jannaschii
This entity is chimeric
Mutation(s): 1 
Gene Names: Tb10.70.3660
UniProt
Find proteins for Q38BM8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38BM8 
Go to UniProtKB:  Q38BM8
Find proteins for Q58576 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58576 
Go to UniProtKB:  Q58576
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ38BM8Q58576
Sequence Annotations
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-13
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description