1JD2

Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A non-covalent Proteasome Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.271 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of the 20 S proteasome:TMC-95A complex: a non-covalent proteasome inhibitor.

Groll, M.Koguchi, Y.Huber, R.Kohno, J.

(2001) J Mol Biol 311: 543-548

  • DOI: 10.1006/jmbi.2001.4869
  • Primary Citation of Related Structures:  
    1JD2

  • PubMed Abstract: 
  • The 20 S proteasome core particle (CP), a multicatalytic protease, is involved in a variety of biologically important processes, including immune response, cell-cycle control, metabolic adaptation, stress response and cell differentiation. Therefore, selective inhibition of the CP will be one possible way to influence these essential pathways ...

    The 20 S proteasome core particle (CP), a multicatalytic protease, is involved in a variety of biologically important processes, including immune response, cell-cycle control, metabolic adaptation, stress response and cell differentiation. Therefore, selective inhibition of the CP will be one possible way to influence these essential pathways. Recently, a new class of specific proteasome inhibitors, TMC-95s, was investigated and we now present a biochemical and crystallographic characterisation of the yeast proteasome core particle in complex with the natural product TMC-95A. This unusual heterocyclic compound specifically blocks the active sites of CPs non-covalently, without modifying the nucleophilic Thr1 residue. The inhibitor is bound to the CP by specific hydrogen bonds with the main-chain atoms of the protein. Analysis of the crystal structure of the complex has revealed which portions of TMC-95s are essential for binding to the proteasome. This will form the basis for the development of synthetic selective proteasome inhibitors as promising candidates for anti-tumoral or anti-inflammatory drugs.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, D-82152, Germany. groll@biochem.mpg.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT Y7A, V250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT Y13B, W244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 3
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PROTEASOME COMPONENT PRE6C, X241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 4
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PROTEASOME COMPONENT PUP2D, Y242Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 5
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PROTEASOME COMPONENT PRE5E, Z233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 6
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PROTEASOME COMPONENT C1AA [auth 1], F244Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 7
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PROTEASOME COMPONENT C7-ALPHABA [auth 2], G243Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46
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Entity ID: 8
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PROTEASOME COMPONENT PUP1H, O222Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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PROTEASOME COMPONENT PUP3I, P204Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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PROTEASOME COMPONENT C11J, Q198Saccharomyces 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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PROTEASOME COMPONENT PRE2K, R212Saccharomyces 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 C5L, S222Saccharomyces cerevisiaeMutation(s): 0 
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 PRE4M, T233Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
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Entity ID: 14
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PROTEASOME COMPONENT PRE3N, U196Saccharomyces 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
TMC-95A inhibitorCA [auth 8], DA [auth 9]5Arthrinium arundinisMutation(s): 0 
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
R4K
Query on R4K
CA [auth 8], DA [auth 9]L-PEPTIDE LINKINGC11 H12 N2 O5TRP
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 15
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001096
Query on PRD_001096
CA [auth 8], DA [auth 9]TMC-95ACyclic peptide /  Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.271 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.2α = 90
b = 301.3β = 112.6
c = 144.8γ = 90
Software Package:
Software NamePurpose
MAR345data collection
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Refinement description