4FZC

20S yeast proteasome in complex with cepafungin I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

One-shot NMR analysis of microbial secretions identifies highly potent proteasome inhibitor.

Stein, M.L.Beck, P.Kaiser, M.Dudler, R.Becker, C.F.Groll, M.

(2012) Proc Natl Acad Sci U S A 109: 18367-18371

  • DOI: 10.1073/pnas.1211423109
  • Primary Citation of Related Structures:  
    4FZC, 4FZG

  • PubMed Abstract: 
  • Natural products represent valuable lead structures for drug discovery. However, for most bioactive compounds no cellular target is yet identified and many substances predicted from genome analysis are inaccessible due to their life stage-dependent biosynthesis, which is not reflected in common isolation procedures ...

    Natural products represent valuable lead structures for drug discovery. However, for most bioactive compounds no cellular target is yet identified and many substances predicted from genome analysis are inaccessible due to their life stage-dependent biosynthesis, which is not reflected in common isolation procedures. In response to these issues, an NMR-based and target-directed protease assay for inhibitor detection of the proteasome was developed. The methodology is suitable for one-shot identification of inhibitors in conglomerates and crude culture broths. The technique was applied for analysis of the different life stages of the bacterium Photorhabdus luminescens, which resulted in the isolation and characterization of cepafungin I (CepI), the strongest proteasome inhibitor described to date. Its biosynthesis is strictly regulated and solely induced by the specific environmental conditions determined by our methodology. The transferability of the developed technique to other drug targets may disclose an abundance of novel compounds applicable for drug development.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Unversität München, 85748 Garching, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y7A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y13B, P244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE6C, Q241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP2D, R242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE5E, S233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C1F, T244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C7-alphaG, U243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP1H, V222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP3I, W204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C11J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE2K, Y212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C5L, Z222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE4M, AA [auth a]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE3N, BA [auth b]196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Cepafungin ICA [auth c], DA [auth d], EA [auth e], FA [auth f]4Saccharomyces cerevisiae S288CMutation(s): 0 
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYO
Query on LYO
CA [auth c], DA [auth d], EA [auth e], FA [auth f]L-PEPTIDE LINKINGC6 H14 N2 O3LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 15
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001018
Query on PRD_001018
CA [auth c], DA [auth d], EA [auth e], FA [auth f]Cepafungin IPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.68α = 90
b = 301.02β = 112.86
c = 144.83γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 2.0: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations, Polymer sequence