5L5Q

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Literature

A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i.

Huber, E.M.Heinemeyer, W.de Bruin, G.Overkleeft, H.S.Groll, M.

(2016) EMBO J 35: 2602-2613

  • DOI: 10.15252/embj.201695222
  • Primary Citation of Related Structures:  
    5L52, 5L55, 5L54, 5L5W, 5L68, 5L5V, 5L67, 5L5Y, 5L5X, 5L69, 5L5Z, 5L5O, 5L60, 5L5Q, 5L62, 5L5P, 5L61, 5L5S, 5L64, 5L5R, 5L63, 5L5U, 5L66, 5L5T, 5L65, 5L5F, 5L5I, 5L5H, 5L5J, 5L5A, 5L5B, 5L5E, 5L5D, 5L6B, 5L6A, 5L6C, 5LTT

  • PubMed Abstract: 
  • Inhibition of the immunoproteasome subunit β5i alleviates autoimmune diseases in preclinical studies and represents a promising new anti-inflammatory therapy. However, the lack of structural data on the human immunoproteasome still hampers drug design. Here, we systematically determined the potency of seven α' β' epoxyketone inhibitors with varying N-caps and P3-stereochemistry for mouse/human β5c/β5i and found pronounced differences in their subunit and species selectivity ...

    Inhibition of the immunoproteasome subunit β5i alleviates autoimmune diseases in preclinical studies and represents a promising new anti-inflammatory therapy. However, the lack of structural data on the human immunoproteasome still hampers drug design. Here, we systematically determined the potency of seven α' β' epoxyketone inhibitors with varying N-caps and P3-stereochemistry for mouse/human β5c/β5i and found pronounced differences in their subunit and species selectivity. Using X-ray crystallography, the compounds were analyzed for their modes of binding to chimeric yeast proteasomes that incorporate key parts of human β5c, human β5i or mouse β5i and the neighboring β6 subunit. The structural data reveal exceptional conformations for the most selective human β5i inhibitors and highlight subtle structural differences as the major reason for the observed species selectivity. Altogether, the presented results validate the humanized yeast proteasome as a powerful tool for structure-based development of β5i inhibitors with potential clinical applications.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie Technische Universität München, Garching, Germany michael.groll@tum.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3B, P258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, Q254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6E, S234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7F, T288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1G, U252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2H, V232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-8,Proteasome subunit beta type-5K, Y211Homo sapiensSaccharomyces cerevisiae S288C
This entity is chimeric
Mutation(s): 0 
Gene Names: PSMB8LMP7PSMB5iRING10Y2PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
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PHAROS:  P28062
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6,Proteasome subunit beta type-6,Proteasome subunit beta type-6,Proteasome subunit beta type-6,Proteasome subunit beta type-6L, Z222Saccharomyces cerevisiae S288CHomo sapiensMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407PSMB1
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7M, AA [auth a]246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1N, BA [auth b]196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6NV (Subject of Investigation/LOI)
Query on 6NV

Download Ideal Coordinates CCD File 
HA [auth K], MA [auth Y]~{N}-[(2~{R})-1-[[(2~{S})-3-(4-methoxyphenyl)-1-[[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-methyl-5~{H}-indene-2-carboxamide
C36 H43 N3 O6
RLIQDSPMEVUJOV-YRIWBWMDSA-N
 Ligand Interaction
MES
Query on MES

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NA [auth Y]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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DA [auth G], LA [auth U]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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CA [auth G], EA [auth I], FA [auth I], GA [auth J], IA [auth K], JA [auth L], KA [auth N], OA [auth Z]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.81α = 90
b = 300.56β = 112.9
c = 145.79γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-05-28 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Groll, M., Huber, E.M.

Funding OrganizationLocationGrant Number
DFGGermanyGR1861/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references