1RYP

CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of 20S proteasome from yeast at 2.4 A resolution.

Groll, M.Ditzel, L.Lowe, J.Stock, D.Bochtler, M.Bartunik, H.D.Huber, R.

(1997) Nature 386: 463-471

  • DOI: 10.1038/386463a0
  • Primary Citation of Related Structures:  
    1RYP

  • PubMed Abstract: 
  • The crystal structure of the 20S proteasome from the yeast Saccharomyces cerevisiae shows that its 28 protein subunits are arranged as an (alpha1...alpha7, beta1...beta7)2 complex in four stacked rings and occupy unique locations. The interior of the particle, which harbours the active sites, is only accessible by some very narrow side entrances ...

    The crystal structure of the 20S proteasome from the yeast Saccharomyces cerevisiae shows that its 28 protein subunits are arranged as an (alpha1...alpha7, beta1...beta7)2 complex in four stacked rings and occupy unique locations. The interior of the particle, which harbours the active sites, is only accessible by some very narrow side entrances. The beta-type subunits are synthesized as proproteins before being proteolytically processed for assembly into the particle. The proforms of three of the seven different beta-type subunits, beta1/PRE3, beta2/PUP1 and beta5/PRE2, are cleaved between the threonine at position 1 and the last glycine of the pro-sequence, with release of the active-site residue Thr 1. These three beta-type subunits have inhibitor-binding sites, indicating that PRE2 has a chymotrypsin-like and a trypsin-like activity and that PRE3 has peptidylglutamyl peptide hydrolytic specificity. Other beta-type subunits are processed to an intermediate form, indicating that an additional nonspecific endopeptidase activity may exist which is important for peptide hydrolysis and for the generation of ligands for class I molecules of the major histocompatibility complex.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsreid, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEA, O243Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEB, P250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEC, Q244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMED, R241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEE, S242Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 6
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20S PROTEASOMEF, T233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 7
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20S PROTEASOMEG, U244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 8
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20S PROTEASOMEH, V205Saccharomyces 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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20S PROTEASOMEI, W222Saccharomyces 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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20S PROTEASOMEJ, X204Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 11
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20S PROTEASOMEK, Y198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEL, Z212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
20S PROTEASOMEAA [auth 1], M222Saccharomyces 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
20S PROTEASOMEBA [auth 2], N233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth A] , DA [auth A] , EA [auth E] , FA [auth G] , GA [auth H] , HA [auth I] , IA [auth J] , JA [auth J] , 
CA [auth A],  DA [auth A],  EA [auth E],  FA [auth G],  GA [auth H],  HA [auth I],  IA [auth J],  JA [auth J],  KA [auth L],  LA [auth M],  MA [auth O],  NA [auth O],  OA [auth S],  PA [auth U],  QA [auth V],  RA [auth W],  SA [auth X],  TA [auth X],  UA [auth Z],  VA [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.286 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.49α = 90
b = 300.7β = 112.89
c = 144.42γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATA)data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance