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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1016/j.cell.2011.12.030
  • Primary Citation of Related Structures:  
    3UN4, 3UN8, 3UNB, 3UNE, 3UNF, 3UNH

  • 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 2.9 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
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
234Mus musculusMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Mus musculusMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
C, Q
248Mus musculusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Mus musculusMutation(s): 0 
UniProt
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UniProt GroupQ9Z2U1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
E, S
263Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9R1P4 (Mus musculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Mus musculusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, U
246Mus musculusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10
H, V
234Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Mus musculusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
201Mus musculusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8
K, Y
204Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, Z
213Mus musculusMutation(s): 0 
UniProt
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UniProt GroupO09061
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
M
219Mus musculusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9BA [auth b],
N
199Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
04C
Query on 04C

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

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

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BC [auth X]
FA [auth B]
FC [auth Z]
GC [auth Z]
HC [auth Z]
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
CL
Query on CL

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AC [auth X]
CA [auth A]
CB [auth N]
DA [auth A]
DB [auth O]
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
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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description