4G4S

Structure of Proteasome-Pba1-Pba2 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a Proteasome Pba1-Pba2 Complex: IMPLICATIONS FOR PROTEASOME ASSEMBLY, ACTIVATION, AND BIOLOGICAL FUNCTION.

Stadtmueller, B.M.Kish-Trier, E.Ferrell, K.Petersen, C.N.Robinson, H.Myszka, D.G.Eckert, D.M.Formosa, T.Hill, C.P.

(2012) J Biol Chem 287: 37371-37382

  • DOI: 10.1074/jbc.M112.367003
  • Primary Citation of Related Structures:  
    4G4S

  • PubMed Abstract: 
  • The 20S proteasome is an essential, 28-subunit protease that sequesters proteolytic sites within a central chamber, thereby repressing substrate degradation until proteasome activators open the entrance/exit gate. Two established activators, Blm10 and PAN/19S, induce gate opening by binding to the pockets between proteasome α-subunits using C-terminal HbYX (hydrophobic-tyrosine-any residue) motifs ...

    The 20S proteasome is an essential, 28-subunit protease that sequesters proteolytic sites within a central chamber, thereby repressing substrate degradation until proteasome activators open the entrance/exit gate. Two established activators, Blm10 and PAN/19S, induce gate opening by binding to the pockets between proteasome α-subunits using C-terminal HbYX (hydrophobic-tyrosine-any residue) motifs. Equivalent HbYX motifs have been identified in Pba1 and Pba2, which function in proteasome assembly. Here, we demonstrate that Pba1-Pba2 proteins form a stable heterodimer that utilizes its HbYX motifs to bind mature 20S proteasomes in vitro and that the Pba1-Pba2 HbYX motifs are important for a physiological function of proteasomes, the maintenance of mitochondrial function. Other factors that contribute to proteasome assembly or function also act in the maintenance of mitochondrial function and display complex genetic interactions with one another, possibly revealing an unexpected pathway of mitochondrial regulation involving the Pba1-Pba2 proteasome interaction. Our determination of a proteasome Pba1-Pba2 crystal structure reveals a Pba1 HbYX interaction that is superimposable with those of known activators, a Pba2 HbYX interaction that is different from those reported previously, and a gate structure that is disrupted but not sufficiently open to allow entry of even small peptides. These findings extend understanding of proteasome interactions with HbYX motifs and suggest multiple roles for Pba1-Pba2 interactions throughout proteasome assembly and function.


    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C7-alphaA252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y7B250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y13C258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE6D254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP2E261Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE5F235Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C1G288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE3H196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP1I232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP3J205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C11K198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE2L212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C5M222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE4N233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome chaperone 1O276Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PBA1POC1YLR199C
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome assembly chaperone 2P269Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ADD66PBA2POC2YKL206C
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Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 18
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000907 (LDZ)
Query on PRD_000907
V [auth L]N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-4-METHYL-1-OXOPENTAN-2-YL]-L-LEUCINAMIDEPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.409α = 90
b = 182.513β = 90
c = 388.782γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references
  • Version 1.2: 2012-11-14
    Changes: Database references
  • Version 1.3: 2013-04-10
    Changes: Non-polymer description