3UNB

Mouse constitutive 20S proteasome in complex with PR-957


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O, c, q
234Mus musculusMutation(s): 0 
Gene Names: Psma2 (Lmpc3)
EC: 3.4.25.1
Find proteins for P49722 (Mus musculus)
Go to UniProtKB:  P49722
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
B, P, d, r
261Mus musculusMutation(s): 0 
Gene Names: Psma4
EC: 3.4.25.1
Find proteins for Q9R1P0 (Mus musculus)
Go to UniProtKB:  Q9R1P0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
C, Q, e, s
248Mus musculusMutation(s): 0 
Gene Names: Psma7
EC: 3.4.25.1
Find proteins for Q9Z2U0 (Mus musculus)
Go to UniProtKB:  Q9Z2U0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R, f, t
241Mus musculusMutation(s): 0 
Gene Names: Psma5
EC: 3.4.25.1
Find proteins for Q9Z2U1 (Mus musculus)
Go to UniProtKB:  Q9Z2U1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
E, S, g, u
263Mus musculusMutation(s): 0 
Gene Names: Psma1
EC: 3.4.25.1
Find proteins for Q9R1P4 (Mus musculus)
Go to UniProtKB:  Q9R1P4
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
F, T, h, v
255Mus musculusMutation(s): 0 
Gene Names: Psma3
EC: 3.4.25.1
Find proteins for O70435 (Mus musculus)
Go to UniProtKB:  O70435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G, U, i, w
246Mus musculusMutation(s): 0 
Gene Names: Psma6
EC: 3.4.25.1
Find proteins for Q9QUM9 (Mus musculus)
Go to UniProtKB:  Q9QUM9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
H, V, j, x
234Mus musculusMutation(s): 0 
Gene Names: Psmb7 (Mmc14)
EC: 3.4.25.1
Find proteins for P70195 (Mus musculus)
Go to UniProtKB:  P70195
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W, k, y
205Mus musculusMutation(s): 0 
Gene Names: Psmb3
EC: 3.4.25.1
Find proteins for Q9R1P1 (Mus musculus)
Go to UniProtKB:  Q9R1P1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
J, X, l, z
201Mus musculusMutation(s): 0 
Gene Names: Psmb2
EC: 3.4.25.1
Find proteins for Q9R1P3 (Mus musculus)
Go to UniProtKB:  Q9R1P3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y, m, 1
205Mus musculusMutation(s): 0 
Gene Names: Psmb5
EC: 3.4.25.1
Find proteins for O55234 (Mus musculus)
Go to UniProtKB:  O55234
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
L, Z, n, 2
213Mus musculusMutation(s): 0 
Gene Names: Psmb1
EC: 3.4.25.1
Find proteins for O09061 (Mus musculus)
Go to UniProtKB:  O09061
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
M, a, o, 3
219Mus musculusMutation(s): 0 
Gene Names: Psmb4 (Lmp3)
EC: 3.4.25.1
Find proteins for P99026 (Mus musculus)
Go to UniProtKB:  P99026
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, b, p, 4
205Mus musculusMutation(s): 0 
Gene Names: Psmb6 (Lmp19)
EC: 3.4.25.1
Find proteins for Q60692 (Mus musculus)
Go to UniProtKB:  Q60692
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
04C
Query on 04C

Download SDF File 
Download CCD File 
1, 4, b, H, j, K, m, N, p, V, x, Y
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 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000991 (04C)
Query on PRD_000991
1,4,b,H,j,K,N,V,Y1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOLPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 171.720α = 90.00
b = 198.590β = 106.59
c = 226.750γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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