5L61

Yeast 20S proteasome with human beta5c (1-138) and human beta6 (99-132) in complex with epoxyketone inhibitor 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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
  • Structures With Same Primary Citation

  • 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 desig ...

    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 LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5,Proteasome subunit beta type-5
K, Y
211Homo sapiensSaccharomyces cerevisiae S288C
This entity is chimeric
Mutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Find proteins for P28074 (Homo sapiens)
Go to UniProtKB:  P28074
NIH Common Fund Data Resources
PHAROS  P28074

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiae S288CHomo sapiensMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Find proteins for P20618 (Homo sapiens)
Go to UniProtKB:  P20618
NIH Common Fund Data Resources
PHAROS  P20618

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
M, a
246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
N, b
196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
C, Q
254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
E, S
234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
F, T
288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
G, U
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
H, V
232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6N5
Query on 6N5

Download CCD File 
K, Y
~{N}-[(2~{S})-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-CFPFVMHBSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
H, K, V, Y
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
G, U
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, G, I, J, K, L, N, Z, b
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.67α = 90
b = 300.68β = 112.84
c = 145.68γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report



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 

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