3UNB

Mouse constitutive 20S proteasome in complex with PR-957


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Immuno- and constitutive proteasome crystal structures reveal differences in substrate and inhibitor specificity.

Huber, E.M.Basler, M.Schwab, R.Heinemeyer, W.Kirk, C.J.Groettrup, M.Groll, M.

(2012) Cell 148: 727-738

  • DOI: 10.1016/j.cell.2011.12.030
  • Primary Citation of Related Structures:  
    3UNE, 3UNF, 3UNH, 3UNB, 3UN4, 3UN8

  • PubMed Abstract: 
  • Constitutive proteasomes and immunoproteasomes shape the peptide repertoire presented by major histocompatibility complex class I (MHC-I) molecules by harboring different sets of catalytically active subunits. Here, we present the crystal structures of constitutive proteasomes and immunoproteasomes from mouse in the presence and absence of the epoxyketone inhibitor PR-957 (ONX 0914) at 2 ...

    Constitutive proteasomes and immunoproteasomes shape the peptide repertoire presented by major histocompatibility complex class I (MHC-I) molecules by harboring different sets of catalytically active subunits. Here, we present the crystal structures of constitutive proteasomes and immunoproteasomes from mouse in the presence and absence of the epoxyketone inhibitor PR-957 (ONX 0914) at 2.9 Å resolution. Based on our X-ray data, we propose a unique catalytic feature for the immunoproteasome subunit β5i/LMP7. Comparison of ligand-free and ligand-bound proteasomes reveals conformational changes in the S1 pocket of β5c/X but not β5i, thereby explaining the selectivity of PR-957 for β5i. Time-resolved structures of yeast proteasome:PR-957 complexes indicate that ligand docking to the active site occurs only via the reactive head group and the P1 side chain. Together, our results support structure-guided design of inhibitory lead structures selective for immunoproteasomes that are linked to cytokine production and diseases like cancer and autoimmune disorders.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O, CA [auth c], QA [auth q]234Mus musculusMutation(s): 0 
Gene Names: Psma2Lmpc3
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B, P, DA [auth d], RA [auth r]261Mus musculusMutation(s): 0 
Gene Names: Psma4
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C, Q, EA [auth e], SA [auth s]248Mus musculusMutation(s): 0 
Gene Names: Psma7
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R, FA [auth f], TA [auth t]241Mus musculusMutation(s): 0 
Gene Names: Psma5
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E, S, GA [auth g], UA [auth u]263Mus musculusMutation(s): 0 
Gene Names: Psma1
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F, T, HA [auth h], VA [auth v]255Mus musculusMutation(s): 0 
Gene Names: Psma3
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G, U, IA [auth i], WA [auth w]246Mus musculusMutation(s): 0 
Gene Names: Psma6
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7H, V, JA [auth j], XA [auth x]234Mus musculusMutation(s): 0 
Gene Names: Psmb7Mmc14
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W, KA [auth k], YA [auth y]205Mus musculusMutation(s): 0 
Gene Names: Psmb3
EC: 3.4.25.1
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2J, X, LA [auth l], ZA [auth z]201Mus musculusMutation(s): 0 
Gene Names: Psmb2
EC: 3.4.25.1
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5AB [auth 1], K, Y, MA [auth m]205Mus musculusMutation(s): 0 
Gene Names: Psmb5
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1BB [auth 2], L, Z, NA [auth n]213Mus musculusMutation(s): 0 
Gene Names: Psmb1
EC: 3.4.25.1
UniProt
Find proteins for O09061 (Mus musculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4CB [auth 3], M, AA [auth a], OA [auth o]219Mus musculusMutation(s): 0 
Gene Names: Psmb4Lmp3
EC: 3.4.25.1
UniProt
Find proteins for P99026 (Mus musculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6DB [auth 4], N, BA [auth b], PA [auth p]205Mus musculusMutation(s): 0 
Gene Names: Psmb6Lmp19
EC: 3.4.25.1
UniProt
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
04C (Subject of Investigation/LOI)
Query on 04C

Download Ideal Coordinates CCD File 
EB [auth H] , FB [auth K] , GB [auth N] , HB [auth V] , IB [auth Y] , JB [auth b] , KB [auth j] , LB [auth m] , 
EB [auth H],  FB [auth K],  GB [auth N],  HB [auth V],  IB [auth Y],  JB [auth b],  KB [auth j],  LB [auth m],  MB [auth p],  NB [auth x],  OB [auth 1],  PB [auth 4]
1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol
C31 H44 N4 O7
SLVOSRJOLWNALP-QAKIEGLASA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 15
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000991 (04C)
Query on PRD_000991
EB [auth H] , FB [auth K] , GB [auth N] , HB [auth V] , IB [auth Y] , JB [auth b] , KB [auth j] , LB [auth m] , 
EB [auth H],  FB [auth K],  GB [auth N],  HB [auth V],  IB [auth Y],  JB [auth b],  KB [auth j],  LB [auth m],  MB [auth p],  NB [auth x],  OB [auth 1],  PB [auth 4]
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOLPeptide-like /  Inhibitor  Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.72α = 90
b = 198.59β = 106.59
c = 226.75γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2013-11-13
    Changes: Structure summary
  • Version 1.4: 2013-11-20
    Changes: Structure summary