1FNT

CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST IN COMPLEX WITH THE PROTEASOME ACTIVATOR PA26 FROM TRYPANOSOME BRUCEI AT 3.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the activation of 20S proteasomes by 11S regulators.

Whitby, F.G.Masters, E.I.Kramer, L.Knowlton, J.R.Yao, Y.Wang, C.C.Hill, C.P.

(2000) Nature 408: 115-120

  • DOI: 10.1038/35040607
  • Primary Citation of Related Structures:  
    1FNT

  • PubMed Abstract: 
  • Most of the non-lysosomal proteolysis that occurs in eukaryotic cells is performed by a nonspecific and abundant barrel-shaped complex called the 20S proteasome. Substrates access the active sites, which are sequestered in an internal chamber, by traversing a narrow opening (alpha-annulus) that is blocked in the unliganded 20S proteasome by amino-terminal sequences of alpha-subunits ...

    Most of the non-lysosomal proteolysis that occurs in eukaryotic cells is performed by a nonspecific and abundant barrel-shaped complex called the 20S proteasome. Substrates access the active sites, which are sequestered in an internal chamber, by traversing a narrow opening (alpha-annulus) that is blocked in the unliganded 20S proteasome by amino-terminal sequences of alpha-subunits. Peptide products probably exit the 20S proteasome through the same opening. 11S regulators (also called PA26 (ref. 4), PA28 (ref. 5) and REG) are heptamers that stimulate 20S proteasome peptidase activity in vitro and may facilitate product release in vivo. Here we report the co-crystal structure of yeast 20S proteasome with the 11S regulator from Trypanosoma brucei (PA26). PA26 carboxy-terminal tails provide binding affinity by inserting into pockets on the 20S proteasome, and PA26 activation loops induce conformational changes in alpha-subunits that open the gate separating the proteasome interior from the intracellular environment. The reduction in processivity expected for an open conformation of the exit gate may explain the role of 11S regulators in the production of ligands for major histocompatibility complex class I molecules.


    Organizational Affiliation

    Biochemistry Department, University of Utah, Salt Lake City 84132, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT C7-ALPHAA, O252Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 2
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PROTEASOME COMPONENT Y7B, P250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 3
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PROTEASOME COMPONENT Y13C, Q245Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 4
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PROTEASOME COMPONENT PRE6D, R254Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT PUP2E, S260Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 6
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PROTEASOME COMPONENT PRE5F, T234Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 7
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PROTEASOME COMPONENT C1G, U287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 8
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PROTEASOME COMPONENT PRE3H, V196Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 9
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PROTEASOME COMPONENT PUP1I, W232Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 10
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PROTEASOME COMPONENT PUP3J, X205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT C11K, Y198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 12
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PROTEASOME COMPONENT PRE2L, Z212Saccharomyces cerevisiaeMutation(s): 1 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 13
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PROTEASOME COMPONENT C5M, AA [auth a]222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT PRE4N, BA [auth b]233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME ACTIVATOR PROTEIN PA26231Trypanosoma bruceiMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.964α = 90
b = 232.127β = 90
c = 296.772γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CCP4model building
DMmodel building
RAVEmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
DMphasing
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation