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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
20S PROTEASOME
A, O
243Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
B, P
250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
C, Q
244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
D, R
241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
E, S
242Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
F, T
233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
G, U
244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
I, W
222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
J, X
204Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
K, Y
198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
L, Z
212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
1, M
222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
2, N
233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
20S PROTEASOME
H, V
205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
1, A, E, G, H, I, J, L, M, O, S, U, V, W, X, Z
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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