3UNF

Mouse 20S immunoproteasome in complex with PR-957


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.2 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, O234Mus musculusMutation(s): 0 
Gene Names: Psma2Lmpc3
UniProt
Find proteins for P49722 (Mus musculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B, P261Mus musculusMutation(s): 0 
Gene Names: Psma4
UniProt
Find proteins for Q9R1P0 (Mus musculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C, Q248Mus musculusMutation(s): 0 
Gene Names: Psma7
UniProt
Find proteins for Q9Z2U0 (Mus musculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R241Mus musculusMutation(s): 0 
Gene Names: Psma5
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E, S263Mus musculusMutation(s): 0 
Gene Names: Psma1
UniProt
Find proteins for Q9R1P4 (Mus musculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F, T255Mus musculusMutation(s): 0 
Gene Names: Psma3
UniProt
Find proteins for O70435 (Mus musculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G, U246Mus musculusMutation(s): 0 
Gene Names: Psma6
UniProt
Find proteins for Q9QUM9 (Mus musculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-10H, V234Mus musculusMutation(s): 0 
Gene Names: Psmb10Lmp10Mecl1
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Mus 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, X201Mus 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-8K, Y204Mus musculusMutation(s): 0 
Gene Names: Psmb8Lmp7Mc13
EC: 3.4.25.1
UniProt
Find proteins for P28063 (Mus musculus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L, Z213Mus 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-4M, AA [auth a]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-9N, BA [auth b]199Mus musculusMutation(s): 0 
Gene Names: Psmb9Lmp2Ring12
EC: 3.4.25.1
UniProt
Find proteins for P28076 (Mus musculus)
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
04C (Subject of Investigation/LOI)
Query on 04C

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AB [auth N], CC [auth Y], JA [auth H], NC [auth b], PA [auth K], RB [auth V]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
IOD
Query on IOD

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BB [auth N], DC [auth Y], KA [auth H], OC [auth b], QA [auth K], SB [auth V]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

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BC [auth X] , FA [auth B] , FC [auth Z] , GC [auth Z] , HC [auth Z] , IA [auth G] , MC [auth a] , NA [auth I] , 
BC [auth X],  FA [auth B],  FC [auth Z],  GC [auth Z],  HC [auth Z],  IA [auth G],  MC [auth a],  NA [auth I],  PB [auth S],  PC [auth b],  RA [auth K],  UA [auth L],  ZA [auth M]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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AC [auth X] , CA [auth A] , CB [auth N] , DA [auth A] , DB [auth O] , EA [auth A] , EB [auth O] , EC [auth Z] , 
AC [auth X],  CA [auth A],  CB [auth N],  DA [auth A],  DB [auth O],  EA [auth A],  EB [auth O],  EC [auth Z],  FB [auth P],  GA [auth D],  GB [auth Q],  HA [auth E],  HB [auth Q],  IB [auth Q],  IC [auth a],  JB [auth Q],  JC [auth a],  KB [auth R],  KC [auth a],  LA [auth H],  LB [auth R],  LC [auth a],  MA [auth I],  MB [auth R],  NB [auth S],  OA [auth J],  OB [auth S],  QB [auth U],  SA [auth L],  TA [auth L],  TB [auth V],  UB [auth V],  VA [auth M],  VB [auth V],  WA [auth M],  WB [auth V],  XA [auth M],  XB [auth W],  YA [auth M],  YB [auth X],  ZB [auth X]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 17
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000991 (04C)
Query on PRD_000991
AB [auth N], CC [auth Y], JA [auth H], NC [auth b], PA [auth K], RB [auth V]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: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.3α = 90
b = 194.6β = 107.1
c = 157.7γ = 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